bims-minimp 2022-02-13 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–02–13
23 papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Spatial and temporal control of mitochondrial H2 O2 release in intact human cells.
Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons.
Proteomic analysis of the mitochondrial glucocorticoid receptor interacting proteins reveals pyruvate dehydrogenase and mitochondrial 60 kDa heat shock protein as potent binding partners.
In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue.
Inhibition of mitoNEET attenuates LPS-induced inflammation and oxidative stress.
TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.
A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics.
Acute exercise rapidly activates hepatic mitophagic flux.
Ribosomal biogenesis regulator DIMT1 controls β-cell protein synthesis, mitochondrial function, and insulin secretion.
Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements.
Mutant C. elegans mitofusin leads to selective removal of mtDNA heteroplasmic deletions across generations to maintain fitness.
NDUFA1 p.Gly32Arg variant in early-onset dementia.
Protein kinase R is an innate immune sensor of proteotoxic stress via accumulation of cytoplasmic IL-24.
Chaperones directly and efficiently disperse stress-triggered biomolecular condensates.
High uric acid induced hippocampal mitochondrial dysfunction and cognitive impairment involving intramitochondrial NF-κB inhibitor α/nuclear factor-κB pathway.
Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach.
New insights into mitochondrial-nuclear interactions revealed through analysis of small RNAs.
Mitochondrial and metabolic dysfunction in ageing and age-related diseases.
Mechanism for the rare fluctuation that powers protein conformational change.
Flaviviridae and mitochondria: Everything you always wanted to know about their relationship but were afraid to ask.
The fate of damaged mitochondrial DNA in the cell.
Perspective: Modulating the integrated stress response to slow aging and ameliorate age-related pathology.
Control of immunity via nutritional interventions.

EMBO J. 2022 Feb 11. e109169

Spatial and temporal control of mitochondrial H2 O2 release in intact human cells.

Michaela Nicole Hoehne, Lianne J H C Jacobs, Kim Jasmin Lapacz, Gaetano Calabrese, Lena Maria Murschall, Teresa Marker, Harshita Kaul, Aleksandra Trifunovic, Bruce Morgan, Mark Fricker, Vsevolod V Belousov, Jan Riemer.

  Hydrogen peroxide (H2 O2 ) has key signaling roles at physiological levels, while causing molecular damage at elevated concentrations. H2 O2 production by mitochondria is implicated in regulating processes inside and outside these organelles. However, it remains unclear whether and how mitochondria in intact cells release H2 O2 . Here, we employed a genetically encoded high-affinity H2 O2 sensor, HyPer7, in mammalian tissue culture cells to investigate different modes of mitochondrial H2 O2 release. We found substantial heterogeneity of HyPer7 dynamics between individual cells. We further observed mitochondria-released H2 O2 directly at the surface of the organelle and in the bulk cytosol, but not in the nucleus or at the plasma membrane, pointing to steep gradients emanating from mitochondria. Gradient formation is controlled by cytosolic peroxiredoxins, which act redundantly and with a substantial reserve capacity. Dynamic adaptation of cytosolic thioredoxin reductase levels during metabolic changes results in improved H2 O2 handling and explains previously observed differences between cell types. Our data suggest that H2 O2 -mediated signaling is initiated only in close proximity to mitochondria and under specific metabolic conditions.

Keywords:  HyPer7; hydrogen peroxide release; mitochondria; peroxiredoxin

DOI:  https://doi.org/10.15252/embj.2021109169
Mol Cell Neurosci. 2022 Feb 04. pii: S1044-7431(22)00010-0. [Epub ahead of print] 103704

Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons.

Nozomu Matsumoto, Ikuma Hori, Masashi K Kajita, Tomoya Murase, Wataru Nakamura, Takahiro Tsuji, Seiji Miyake, Masaru Inatani, Yoshiyuki Konishi.

  In the central nervous system (CNS), many neurons develop axonal arbors that are crucial for information processing. Previous studies have demonstrated that premature axons contain motile and stationary mitochondria, and their balance is important for axonal arborization. However, the mechanisms by which neurons determine the positions of stationary mitochondria as well as their turnover remain to be elucidated. We observed that the distribution of stationary mitochondrial spots along the unmyelinated and nonsynaptic axons is not random but rather relatively uniform both in primary cultured neurons and in tissues. Intriguingly, whereas the positions of each mitochondrial spot changed over time, the overall distribution remained uniform. In addition, local inactivation of mitochondria by KillerRed mediated chromophore-assisted light inactivation (CALI) inhibited the translocation of mitochondrial spots in adjacent axonal regions, suggesting that functional mitochondria enhance the motility of other mitochondria in the vicinity. Signals of ATP:ADP sensor, PercevalHR indicated that the ATP:ADP ratio was relatively high around mitochondria, and treating axons with phosphocreatine (PCr), which supplies ATP, reduced the immobile mitochondria induced by the local mitochondrial inactivation. In a mathematical model, we found that the ATP gradient generated by mitochondria, and ATP dependent regulation of mitochondrial motility could establish uniform mitochondrial distribution. These observations suggest that axons in the CNS possess the system that distributes mitochondria uniformly, and intermitochondrial signaling contribute to the regulation. In addition, our results suggest the possibility that ATP might be one of the molecules mediating the signaling.

Keywords:  ATP; Axonal transport; Cerebellar granule neurons; Mitochondrial distribution; Retinal ganglion cells; Stationary mitochondria

DOI:  https://doi.org/10.1016/j.mcn.2022.103704
J Proteomics. 2022 Feb 03. pii: S1874-3919(22)00032-X. [Epub ahead of print] 104509

Proteomic analysis of the mitochondrial glucocorticoid receptor interacting proteins reveals pyruvate dehydrogenase and mitochondrial 60 kDa heat shock protein as potent binding partners.

Aikaterini G Karra, Aikaterini Sioutopoulou, Vyron Gorgogietas, Martina Samiotaki, George Panayotou, Anna-Maria G Psarra.

  Glucocorticoids are steroid hormones that regulate plethora biological actions such as growth and metabolism, immune response, and apoptosis. Glucocorticoids actions are mediated via glucocorticoid receptors which act mainly as transcription factors, but it is also found to be localized in mitochondria. Mitochondrial localization of the receptor indicates novel functions of the receptor. Characterization of the mitochondrial glucocorticoid receptor (mtGR) interacting proteins will shed light on these actions and the biochemical mechanisms that underlie mitochondrial glucocorticoid receptor import and functions. In this study, applying immunoprecipitation, mass spectrometry and Western blot analysis of the GR interacting proteins in total or mitochondrial extracts of HepG2 cells and of HepG2 cells overexpressing a mitochondrial targeted GR we found pyruvate dehydrogenase (PDH), chaperones such as and heat shock protein (HSP) -60, -70, -75 and -90, and 78 kDa glucose-regulated protein, mitochondrial transcription factors and enzymes involved in the regulation of the mitochondrial protein biosynthesis, lipid metabolism, ATP production and apoptosis as glucocorticoid receptor interacting proteins. Our results uncover potential novel mitochondrial partners of the receptor, suggesting possible new regulatory roles of mtGR in the control of mitochondrial-associated functions of the cell. SIGNIFICANCE: In this study the mitochondrial GR interacting proteins were characterized highlighting novel regulatory roles of the receptor in mitochondria. Detection of the mtGR/PDH and mtGR/HSP60 interaction in almost all the analyses performed uncovered PDH and HSP60 proteins as potent mtGR binding partners. The interesting finding of the PDH/mtGR interaction possibly indicates involvement of mtGR in the regulation of the balance between glycolytic and oxidative phosphorylation energy production. Characterization of the mitochondrial heat shock 60, -70, 75 and 78 proteins as mtGR binding partners contribute to the characterization of the biochemical mechanisms of the mitochondrial import of the receptor. Moreover, identification of mitochondrial heat shock proteins, metabolic enzymes, transcription factors, OXPHOS, and regulatory molecules in mitochondrial protein biosynthesis as mtGR binding partners indicates possible new regulatory roles of mtGR in the glucocorticoids-induced regulation and orchestration of nuclear and mitochondrial functions, the exact biochemical mechanism of which remain to be established. The study discloses potential new regulatory roles of the receptor in mitochondria, pointing out its importance as a promising target molecule for the control of the mitochondria-associated pathophysiology of the cell.

Keywords:  Apoptosis; Energy production; Glucocorticoid receptor; Heat shock proteins; Mitochondria; Pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.jprot.2022.104509
Nat Commun. 2022 Feb 08. 13(1): 750

In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue.

Pedro Silva-Pinheiro, Pavel A Nash, Lindsey Van Haute, Christian D Mutti, Keira Turner, Michal Minczuk.

Mitochondria host key metabolic processes vital for cellular energy provision and are central to cell fate decisions. They are subjected to unique genetic control by both nuclear DNA and their own multi-copy genome - mitochondrial DNA (mtDNA). Mutations in mtDNA often lead to clinically heterogeneous, maternally inherited diseases that display different organ-specific presentation at any stage of life. For a long time, genetic manipulation of mammalian mtDNA has posed a major challenge, impeding our ability to understand the basic mitochondrial biology and mechanisms underpinning mitochondrial disease. However, an important new tool for mtDNA mutagenesis has emerged recently, namely double-stranded DNA deaminase (DddA)-derived cytosine base editor (DdCBE). Here, we test this emerging tool for in vivo use, by delivering DdCBEs into mouse heart using adeno-associated virus (AAV) vectors and show that it can install desired mtDNA edits in adult and neonatal mice. This work provides proof-of-concept for use of DdCBEs to mutagenize mtDNA in vivo in post-mitotic tissues and provides crucial insights into potential translation to human somatic gene correction therapies to treat primary mitochondrial disease phenotypes.

DOI: https://doi.org/10.1038/s41467-022-28358-w
Cell Death Dis. 2022 Feb 08. 13(2): 127

Inhibition of mitoNEET attenuates LPS-induced inflammation and oxidative stress.

Seunghee Lee, Byeong Geun Seok, Seon-Jin Lee, Su Wol Chung.

MitoNEET (mitochondrial protein containing Asn-Glu-Glu-Thr (NEET) sequence) is a 2Fe-2S cluster-containing integral membrane protein that resides in the mitochondrial outer membrane and participates in a redox-sensitive signaling and Fe-S cluster transfer. Thus, mitoNEET is a key regulator of mitochondrial oxidative capacity and iron homeostasis. Moreover, mitochondrial dysfunction and oxidative stress play critical roles in inflammatory diseases such as sepsis. Increased iron levels mediated by mitochondrial dysfunction lead to oxidative damage and generation of reactive oxygen species (ROS). Increasing evidence suggests that targeting mitoNEET to reverse mitochondrial dysfunction deserves further investigation. However, the role of mitoNEET in inflammatory diseases is unknown. Here, we investigated the mechanism of action and function of mitoNEET during lipopolysaccharide (LPS)-induced inflammatory responses in vitro and in vivo. Levels of mitoNEET protein increased during microbial or LPS-induced sepsis. Pharmacological inhibition of mitoNEET using mitoNEET ligand-1 (NL-1) decreased the levels of pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α in animal models of sepsis, as well as LPS-induced inflammatory responses by macrophages in vitro. Inhibition of mitoNEET using NL-1 or mitoNEET shRNA abrogated LPS-induced ROS formation and mitochondrial dysfunction. Furthermore, mitochondrial iron accumulation led to generation of LPS-induced ROS, a process blocked by NL-1 or shRNA. Taken together, these data suggest that mitoNEET could be a key therapeutic molecule that targets mitochondrial dysfunction during inflammatory diseases and sepsis.

DOI: https://doi.org/10.1038/s41419-022-04586-2
Proc Natl Acad Sci U S A. 2022 Feb 15. pii: e2113454119. [Epub ahead of print]119(7):

TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation.

Di Liu, Zhiyao Zhao, Yuanchu She, Lei Zhang, Xiangtian Chen, Ling Ma, Jun Cui.

  Autophagy is a fundamental cellular process of protein degradation and recycling that regulates immune signaling pathways via multiple mechanisms. However, it remains unclear how autophagy epigenetically regulates the immune response. Here, we identified TRIM14 as an epigenetic regulator that reduces histone H3K9 trimethylation by inhibiting the autophagic degradation of the histone demethylase KDM4D. TRIM14 recruited the deubiquitinases USP14 and BRCC3 to cleave the K63-linked ubiquitin chains of KDM4D, which prevented KDM4D from undergoing optineurin (OPTN)-mediated selective autophagy. Tripartite motif-containing 14 (TRIM14) deficiency in dendritic cells significantly impaired the expression of the KDM4D-directed proinflammatory cytokines interleukin 12 (Il12) and Il23 and protected mice from autoimmune inflammation. Taken together, these findings highlight the cross-talk between epigenetic regulation and autophagy and suggest TRIM14 is a potential target of therapeutic intervention for inflammation-related diseases.

Keywords:  KDM4D; TRIM14; autophagy; epigenetic regulation; inflammation

DOI:  https://doi.org/10.1073/pnas.2113454119
Proc Natl Acad Sci U S A. 2022 Feb 15. pii: e2121491119. [Epub ahead of print]119(7):

A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics.

Ola Karmi, Henri-Baptiste Marjault, Fang Bai, Susmita Roy, Yang-Sung Sohn, Merav Darash Yahana, Faruck Morcos, Konstantinos Ioannidis, Yaakov Nahmias, Patricia A Jennings, Ron Mittler, José N Onuchic, Rachel Nechushtai.

  Mitochondrial inner NEET (MiNT) and the outer mitochondrial membrane (OMM) mitoNEET (mNT) proteins belong to the NEET protein family. This family plays a key role in mitochondrial labile iron and reactive oxygen species (ROS) homeostasis. NEET proteins contain labile [2Fe-2S] clusters which can be transferred to apo-acceptor proteins. In eukaryotes, the biogenesis of [2Fe-2S] clusters occurs within the mitochondria by the iron-sulfur cluster (ISC) system; the clusters are then transferred to [2Fe-2S] proteins within the mitochondria or exported to cytosolic proteins and the cytosolic iron-sulfur cluster assembly (CIA) system. The last step of export of the [2Fe-2S] is not yet fully characterized. Here we show that MiNT interacts with voltage-dependent anion channel 1 (VDAC1), a major OMM protein that connects the intermembrane space with the cytosol and participates in regulating the levels of different ions including mitochondrial labile iron (mLI). We further show that VDAC1 is mediating the interaction between MiNT and mNT, in which MiNT transfers its [2Fe-2S] clusters from inside the mitochondria to mNT that is facing the cytosol. This MiNT-VDAC1-mNT interaction is shown both experimentally and by computational calculations. Additionally, we show that modifying MiNT expression in breast cancer cells affects the dynamics of mitochondrial structure and morphology, mitochondrial function, and breast cancer tumor growth. Our findings reveal a pathway for the transfer of [2Fe-2S] clusters, which are assembled inside the mitochondria, to the cytosol.

Keywords:  CISD3; VDAC1; [2Fe-2S] cluster; mitoNEET; mitochondrial inner NEET protein (MiNT)

DOI:  https://doi.org/10.1073/pnas.2121491119
J Appl Physiol (1985). 2022 Feb 10.

Acute exercise rapidly activates hepatic mitophagic flux.

Colin S McCoin, Edziu Franczak, Fengyan Deng, Dong Pei, Wen-Xing Ding, John P Thyfault.

  Exercise is critical for improving metabolic health and putatively maintains or enhances mitochondrial quality control in metabolic tissues. While previous work has shown exercise elicits hepatic mitochondrial biogenesis, it is unknown if acute exercise activates hepatic mitophagy, the selective degradation of damaged or low-functioning mitochondria. We tested if an acute bout of treadmill running increased hepatic mitophagic flux both immediately after and 2 hours post-exercise in 15-24-week-old C57BL/6J female mice. Acute exercise did not significantly increase markers of autophagic flux, however, mitophagic flux was activated 2 hours post-treadmill running as measured by accumulation of both LC3-II and p62 in isolated mitochondria in the presence of leupeptin, an inhibitor of autophagosome degradation. Further, mitochondrial associated ubiquitin, which recruits the autophagy receptor protein p62, was also significantly increased at 2 hours. Further examination via western blot and proteomics analysis revealed acute exercise elicits a time-dependent, dynamic activation of mitophagy pathways. Moreover, the results suggest that exercise induced hepatic mitophagy is likely mediated by both poly-ubiquitination and receptor mediated signaling pathways. Overall, we provide evidence that acute exercise activates hepatic mitophagic flux while also revealing specific receptor-mediated proteins by which exercise maintains mitochondrial quality control in the liver.

Keywords:  Exercise; Liver; Mitochondria; Mitophagic Flux; Mitophagy

DOI:  https://doi.org/10.1152/japplphysiol.00704.2021
J Biol Chem. 2022 Feb 08. pii: S0021-9258(22)00132-6. [Epub ahead of print] 101692

Ribosomal biogenesis regulator DIMT1 controls β-cell protein synthesis, mitochondrial function, and insulin secretion.

Gaurav Verma, Alexander Bowen, Sevda Gheibi, Alexander Hamilton, Sowndarya Muthukumar, Luis Rodrigo Cataldo, Olof Asplund, Jonathan Esguerra, Alexandros Karagiannopoulos, Claire Lyons, Elaine Cowan, Cristian Bellodi, Rashmi Prasad, Malin Fex, Hindrik Mulder.

  We previously reported that loss of mitochondrial transcription factor B1 (TFB1M) leads to mitochondrial dysfunction and is involved in the pathogenesis of type 2 diabetes (T2D). Whether defects in ribosomal processing impact mitochondrial function and could play a pathogenetic role in β-cells and T2D is not known. To this end, we explored expression and the functional role of dimethyladenosine transferase 1 homolog (DIMT1), a homolog of TFB1M and a ribosomal RNA (rRNA) methyltransferase implicated in the control of rRNA. Expression of DIMT1 was increased in human islets from T2D donors and correlated positively with expression of insulin mRNA, but negatively with insulin secretion. We show that silencing of DIMT1 in insulin-secreting cells impacted mitochondrial function, leading to lower expression of mitochondrial OXPHOS proteins, reduced oxygen consumption rate, dissipated mitochondrial membrane potential, and a slower rate of ATP production. In addition, the rate of protein synthesis was retarded upon DIMT1-deficiency. Consequently, we found that DIMT1 deficiency led to perturbed insulin secretion in rodent cell lines and islets, as well as in a human β-cell line. We observed defects in rRNA processing and reduced interactions between NIN1 (RPN12) binding protein 1 homolog (NOB-1) and Pescadillo ribosomal biogenesis factor 1 (PES-1), critical ribosomal subunit RNA proteins, the dysfunction of which may play a part in disturbing protein synthesis in β-cells. In conclusion, DIMT1 deficiency perturbs protein synthesis, resulting in mitochondrial dysfunction and disrupted insulin secretion, both potential pathogenetic processes in T2D.

Keywords:  DIMT1; Diabetes; Methyltransferase; Mitochondria; Ribosomes

DOI:  https://doi.org/10.1016/j.jbc.2022.101692
J Biol Chem. 2022 Feb 07. pii: S0021-9258(22)00134-X. [Epub ahead of print] 101694

Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements.

Jie Yang, Albert S Song, R Luke Wiseman, Gabriel C Lander.

  Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly, and is uniquely characterized by a ∼50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-EM structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a ∼15-residue C-terminal extension. These additional C-terminal residues form an alpha-helix that is located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1's enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function.

Keywords:  AAA+ protease; ATP-dependent protease; Lon; cryo-electron microscopy; enzyme structure; mitochondria; proteostasis

DOI:  https://doi.org/10.1016/j.jbc.2022.101694
BMC Biol. 2022 Feb 09. 20(1): 40

Mutant C. elegans mitofusin leads to selective removal of mtDNA heteroplasmic deletions across generations to maintain fitness.

Lana Meshnik, Dan Bar-Yaacov, Dana Kasztan, Tali Neiger, Tal Cohen, Mor Kishner, Itay Valenci, Sara Dadon, Christopher J Klein, Jeffery M Vance, Yoram Nevo, Stephan Züchner, Ofer Ovadia, Dan Mishmar, Anat Ben-Zvi.

   BACKGROUND: Mitochondrial DNA (mtDNA) is present at high copy numbers in animal cells, and though characterized by a single haplotype in each individual due to maternal germline inheritance, deleterious mutations and intact mtDNA molecules frequently co-exist (heteroplasmy). A number of factors, such as replicative segregation, mitochondrial bottlenecks, and selection, may modulate the exitance of heteroplasmic mutations. Since such mutations may have pathological consequences, they likely survive and are inherited due to functional complementation via the intracellular mitochondrial network. Here, we hypothesized that compromised mitochondrial fusion would hamper such complementation, thereby affecting heteroplasmy inheritance.
RESULTS: We assessed heteroplasmy levels in three Caenorhabditis elegans strains carrying different heteroplasmic mtDNA deletions (ΔmtDNA) in the background of mutant mitofusin (fzo-1). Animals displayed severe embryonic lethality and developmental delay. Strikingly, observed phenotypes were relieved during subsequent generations in association with complete loss of ΔmtDNA molecules. Moreover, deletion loss rates were negatively correlated with the size of mtDNA deletions, suggesting that mitochondrial fusion is essential and sensitive to the nature of the heteroplasmic mtDNA mutations. Introducing the ΔmtDNA into a fzo-1;pdr-1;+/ΔmtDNA (PARKIN ortholog) double mutant resulted in a skewed Mendelian progeny distribution, in contrast to the normal distribution in the fzo-1;+/ΔmtDNA mutant, and severely reduced brood size. Notably, the ΔmtDNA was lost across generations in association with improved phenotypes.
CONCLUSIONS: Taken together, our findings show that when mitochondrial fusion is compromised, deleterious heteroplasmic mutations cannot evade natural selection while inherited through generations. Moreover, our findings underline the importance of cross-talk between mitochondrial fusion and mitophagy in modulating the inheritance of mtDNA heteroplasmy.

Keywords:  C. elegans; Heteroplasmy inheritance; Mitofusin; PARKIN; fzo-1; mtDNA; pdr-1

DOI:  https://doi.org/10.1186/s12915-022-01241-2
Neurobiol Aging. 2022 Jan 21. pii: S0197-4580(22)00012-4. [Epub ahead of print]

NDUFA1 p.Gly32Arg variant in early-onset dementia.

Samuli Huttula, Henri Väyrynen, Seppo Helisalmi, Laura Kytövuori, Laura Luukkainen, Mikko Hiltunen, Anne M Remes, Johanna Krüger.

  Early-onset dementia (EOD) is highly heritable. However, in many EOD cases the genetic etiology remains unknown. Mitochondrial dysfunction is associated with neurodegeneration and the complex I (CI) deficiency is the most common enzyme deficiency in diseases related to oxidative phosphorylation. The X-chromosomal NDUFA1 gene is essential for the activity of CI. Mutations in NDUFA1 are associated with mitochondrial diseases especially with Leigh syndrome. CI deficiency is also associated with neurodegenerative diseases, such as Alzheimer's disease (AD). The aim of this study was to evaluate the role of NDUFA1 variants in EOD patients. Next-generation sequencing panel was used to screen NDUFA1 variants in a cohort of 37 EOD patients with a family history of dementia or an atypical or rapidly progressive course of disease. We identified a hemizygous p.Gly32Arg variant in two brothers with AD. Subsequent screening of the variant in a larger cohort of EOD patients (n = 279) revealed three additional variant carriers (one male and two heterozygote females), suggesting that NDUFA1 variant p.Gly32Arg may play a role in neurodegenerative dementia.

Keywords:  Alzheimer's disease; Dementia; Mitochondria; NDUFA1; Neurodegeneration; OXPHOS

DOI:  https://doi.org/10.1016/j.neurobiolaging.2021.09.026
Sci Immunol. 2022 Feb 11. 7(68): eabi6763

Protein kinase R is an innate immune sensor of proteotoxic stress via accumulation of cytoplasmic IL-24.

Sophia Davidson, Chien-Hsiung Yu, Annemarie Steiner, Frédéric Ebstein, Paul J Baker, Valentina Jarur-Chamy, Katja Hrovat Schaale, Pawat Laohamonthonkul, Klara Kong, Dale J Calleja, Cassandra R Harapas, Katherine R Balka, Jacob Mitchell, Jacob T Jackson, Niall D Geoghegan, Fiona Moghaddas, Kelly L Rogers, Katrin D Mayer-Barber, Adriana A De Jesus, Dominic De Nardo, Benjamin T Kile, Anthony J Sadler, M Cecilia Poli, Elke Krüger, Raphaela Goldbach Mansky, Seth L Masters.

Proteasome dysfunction can lead to autoinflammatory disease associated with elevated type I interferon (IFN-αβ) and NF-κB signaling; however, the innate immune pathway driving this is currently unknown. Here, we identified protein kinase R (PKR) as an innate immune sensor for proteotoxic stress. PKR activation was observed in cellular models of decreased proteasome function and in multiple cell types from patients with proteasome-associated autoinflammatory disease (PRAAS). Furthermore, genetic deletion or small-molecule inhibition of PKR in vitro ameliorated inflammation driven by proteasome deficiency. In vivo, proteasome inhibitor-induced inflammatory gene transcription was blunted in PKR-deficient mice compared with littermate controls. PKR also acted as a rheostat for proteotoxic stress by triggering phosphorylation of eIF2α, which can prevent the translation of new proteins to restore homeostasis. Although traditionally known as a sensor of RNA, under conditions of proteasome dysfunction, PKR sensed the cytoplasmic accumulation of a known interactor, interleukin-24 (IL-24). When misfolded IL-24 egress into the cytosol was blocked by inhibition of the endoplasmic reticulum-associated degradation pathway, PKR activation and subsequent inflammatory signaling were blunted. Cytokines such as IL-24 are normally secreted from cells; therefore, cytoplasmic accumulation of IL-24 represents an internal danger-associated molecular pattern. Thus, we have identified a mechanism by which proteotoxic stress is detected, causing inflammation observed in the disease PRAAS.

DOI: https://doi.org/10.1126/sciimmunol.abi6763
Mol Cell. 2022 Feb 08. pii: S1097-2765(22)00005-3. [Epub ahead of print]

Chaperones directly and efficiently disperse stress-triggered biomolecular condensates.

Haneul Yoo, Jared A M Bard, Evgeny V Pilipenko, D Allan Drummond.

  Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.

Keywords:  biomolecular condensates; cell stress; disaggregation; heat shock; molecular chaperones; stress response

DOI:  https://doi.org/10.1016/j.molcel.2022.01.005
Neuroreport. 2022 Feb 02. 33(3): 109-115

High uric acid induced hippocampal mitochondrial dysfunction and cognitive impairment involving intramitochondrial NF-κB inhibitor α/nuclear factor-κB pathway.

Chun Shi, Han Guo, Xintong Liu.

OBJECTIVES: Epidemiological research has indicated that hyperuricemia may impair cognitive ability; however, the underlying mechanisms remain unclear. The present study thus investigated the possible mechanism underlying hyperuricemia-related cognitive impairment.
METHODS: Using hyperuricemic rats and high uric acid (UA) intracerebroventricularly treated mice, the current study elucidated whether and how high UA impaired cognitive ability and hippocampal mitochondrial bioenergetic function.
RESULTS: Hyperuricemia induced UA uptake by hippocampal mitochondria, which impaired cognitive ability and disrupted the bioenergetic function of hippocampal mitochondria, indicated by reduced ATP production and decreased cytochrome c oxidase (COX) activity. Mechanistically, excess UA might trigger intramitochondrial NF-κB inhibitor α (IκBα)/nuclear factor-κB (NF-κB) pathway to downregulate the subunit III of COX (COXIII).
CONCLUSION: The results provided new insights into the mechanism underlying hyperuricemia-related cognitive decline.

DOI: https://doi.org/10.1097/WNR.0000000000001762
Protein Sci. 2022 Feb 08.

Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach.

Kyle P Smith, Woonghee Lee, Marco Tonelli, Yeongjoon Lee, Samuel H Light, Gabriel Cornilescu, Srinivas Chakravarthy.

  The bacterial pathogen Vibrio cholerae use a type III secretion system to inject effector proteins into a host cell. Recently, a putative Toxic GTPase Activating Protein (ToxGAP) called VopE was identified as a T3SS substrate and virulence factor that affected host mitochondrial dynamics and immune response. However, biophysical and structural characterization has been absent. Here, we describe solution NMR structure of the putative GAP domain (73-204) of VopE. Using SEC-SAXS and RDC data, we restrained the MD process to efficiently determine the overall fold and improve the quality of the output calculated structures. Comparing the structure of VopE with other ToxGAP's revealed a similar overall fold with several features unique to VopE. Specifically, the "Bulge 1", α1 helix, and noteworthy "backside linker" elements on the N-terminus are dissimilar to the other ToxGAP's. By using NMR relaxation dispersion experiments, we demonstrate that these regions undergo motions on a >6 s-1 timescale. Based on the disposition of these mobile regions relative to the putative catalytic arginine residue, we hypothesize the protein may undergo structural changes to bind cognate GTPases. This article is protected by copyright. All rights reserved.

Keywords:  ExoS; GTP hydrolysis; T3SS secretion system; Vibrio Cholerae; YopE; catalytic arginine finger; helical bundle; mitochondrial dynamics; relaxation dispersion; small-angle x-ray scattering

DOI:  https://doi.org/10.1002/pro.4282
Genome Biol Evol. 2022 Feb 10. pii: evac023. [Epub ahead of print]

New insights into mitochondrial-nuclear interactions revealed through analysis of small RNAs.

Andrea Pozzi, Damian K Dowling.

  Mitochondrial sequence variants affect phenotypic function, often through interaction with the nuclear genome. These "mitonuclear" interactions have been linked both to evolutionary processes and human health. The study of these interactions has focused on mechanisms regulating communication between mitochondrial and nuclear proteins; the role of mitochondrial (mt) RNAs has received little attention. Here, we show that small mt-RNAs bind to the nuclear protein Argonaute 2, and that nuclear miRNAs bind to mt-mRNAs. We identify one small mt-RNA that binds to Argonaute 2 in human tissues whose expression and sequence remain unchanged across vertebrates. While analyses of CLEAR-CLIP sequencing datasets of human and mouse did not reveal consistent interactions between small mt-RNAs and nuclear mRNAs, we found that MT-ND4 and MT-ATP6 mRNAs are bound by different nuclear miRNAs in humans and mice. Our work homes in on previously unknown interactions between nuclear and small mt-RNAs, which may play key roles in intergenomic communication.

Keywords:  AGO2; Mitonuclear communication; mitochondria; mtDNA; small RNAs

DOI:  https://doi.org/10.1093/gbe/evac023
Nat Rev Endocrinol. 2022 Feb 10.

Mitochondrial and metabolic dysfunction in ageing and age-related diseases.

João A Amorim, Giuseppe Coppotelli, Anabela P Rolo, Carlos M Palmeira, Jaime M Ross, David A Sinclair.

Organismal ageing is accompanied by progressive loss of cellular function and systemic deterioration of multiple tissues, leading to impaired function and increased vulnerability to death. Mitochondria have become recognized not merely as being energy suppliers but also as having an essential role in the development of diseases associated with ageing, such as neurodegenerative and cardiovascular diseases. A growing body of evidence suggests that ageing and age-related diseases are tightly related to an energy supply and demand imbalance, which might be alleviated by a variety of interventions, including physical activity and calorie restriction, as well as naturally occurring molecules targeting conserved longevity pathways. Here, we review key historical advances and progress from the past few years in our understanding of the role of mitochondria in ageing and age-related metabolic diseases. We also highlight emerging scientific innovations using mitochondria-targeted therapeutic approaches.

DOI: https://doi.org/10.1038/s41574-021-00626-7
J Chem Phys. 2022 Feb 07. 156(5): 054119

Mechanism for the rare fluctuation that powers protein conformational change.

Shanshan Wu, Ao Ma.

Most functional processes of biomolecules are rare events. Key to a rare event is the rare fluctuation that enables the energy activation process that precedes and powers crossing of the activation barrier. However, the physical nature of this rare fluctuation and how it enables energy activation and subsequently barrier crossing are unknown. We developed a novel metric, the reaction capacity pC, that rigorously defines the beginning and parameterizes the progress of energy activation. This enabled us to identify the rare fluctuation as a special phase-space condition that is necessary and sufficient for initiating systematic energy flow from the non-reaction coordinates into the reaction coordinates. The energy activation of a prototype biomolecular isomerization reaction is dominated by kinetic energy transferring into and accumulating in the reaction coordinates, administered by inertial forces alone. This mechanism for energy activation is fundamentally different from the mechanism suggested by Kramers theory.

DOI: https://doi.org/10.1063/5.0077444
Virologie (Montrouge). 2022 Feb 10.

Flaviviridae and mitochondria: Everything you always wanted to know about their relationship but were afraid to ask.

Wesley Freppel, Marie Roy, Laurent Chatel-Chaix.

  Infections with Flaviviridae constitute a major public health concern, especially considering the limited availability of prophylactic and therapeutic treatments. Most notably, the recent emergence of Zika virus in the Americas was associated with the dramatic increase of severe symptoms such as congenital microcephaly, while hepatitis C virus causes the death of approximately 300,000 individuals annually. Flaviviridae have evolved to hijack cellular organelles and to favor their replication, often via divergent molecular mechanisms. In addition to the remodeling of the endoplasmic reticulum, which is required for the replication of the viral genome and the assembly of the neosynthesized virions, Flaviviridae induce drastic morphological alterations of the mitochondria. This is associated with the viral co-opting of several key mitochondrial functions in apoptosis, innate immunity and metabolism. This review recapitulates the current knowledge about the morphological and functional relationship between Flaviviridae and mitochondria and explains how this contributes to the establishment of a cytoplasmic environment which is favorable to viral replication.

Keywords:  apoptosis; flavivirus; hepatitis C virus; innate immunity; mitochondria; mitochondria morphodynamics

DOI:  https://doi.org/10.1684/vir.2022.0926
Biochim Biophys Acta Mol Cell Res. 2022 Feb 04. pii: S0167-4889(22)00024-6. [Epub ahead of print] 119233

The fate of damaged mitochondrial DNA in the cell.

Siyang Liao, Li Chen, Zhiyin Song, He He.

  Mitochondrion is a double membrane organelle that is responsible for cellular respiration and production of most of the ATP in eukaryotic cells. Mitochondrial DNA (mtDNA) is the genetic material carried by mitochondria, which encodes some essential subunits of respiratory complexes independent of nuclear DNA. Normally, mtDNA binds to certain proteins to form a nucleoid that is stable in mitochondria. Nevertheless, a variety of physiological or pathological stresses can cause mtDNA damage, and the accumulation of damaged mtDNA in mitochondria leads to mitochondrial dysfunction, which triggers the occurrence of mitochondrial diseases in vivo. In response to mtDNA damage, cell initiates multiple pathways including mtDNA repair, degradation, clearance and release, to recover mtDNA, and maintain mitochondrial quality and cell homeostasis. In this review, we provide our current understanding of the fate of damaged mtDNA, focus on the pathways and mechanisms of removing damaged mtDNA in the cell.

Keywords:  Mitochondria DNA (mtDNA); Mitocytosis; Mitophagy; mtDNA release

DOI:  https://doi.org/10.1016/j.bbamcr.2022.119233
Nat Aging. 2021 Sep;1(9): 760-768

Perspective: Modulating the integrated stress response to slow aging and ameliorate age-related pathology.

Maxime J Derisbourg, Matías D Hartman, Martin S Denzel.

Healthy aging requires the coordination of numerous stress signaling pathways that converge on the protein homeostasis network. The Integrated Stress Response (ISR) is activated by diverse stimuli, leading to phosphorylation of the eukaryotic translation initiation factor elF2 in its α-subunit. Under replete conditions, elF2 orchestrates 5' cap-dependent mRNA translation and is thus responsible for general protein synthesis. elF2α phosphorylation, the key event of the ISR, reduces global mRNA translation while enhancing the expression of a signature set of stress response genes. Despite the critical role of protein quality control in healthy aging and in numerous longevity pathways, the role of the ISR in longevity remains largely unexplored. ISR activity increases with age, suggesting a potential link with the aging process. Although decreased protein biosynthesis, which occurs during ISR activation, have been linked to lifespan extension, recent data show that lifespan is limited by the ISR as its inhibition extends survival in nematodes and enhances cognitive function in aged mice. Here we survey how aging affects the ISR, the role of the ISR in modulating aging, and pharmacological interventions to tune the ISR. Finally, we will explore the ISR as a plausible target for clinical interventions in aging and age-related disease.

DOI: https://doi.org/10.1038/s43587-021-00112-9
Immunity. 2022 Feb 08. pii: S1074-7613(22)00033-4. [Epub ahead of print]55(2): 210-223

Control of immunity via nutritional interventions.

Nicholas Collins, Yasmine Belkaid.

  Nutrition affects all physiological processes including those linked to the development and function of our immune system. Here, we discuss recent evidence and emerging concepts supporting the idea that our newfound relationship with nutrition in industrialized countries has fundamentally altered the way in which our immune system is wired. This will be examined through the lens of studies showing that mild or transient reductions in dietary intake can enhance protective immunity while also limiting aberrant inflammatory responses. We will further discuss how trade-offs and priorities begin to emerge in the context of severe nutritional stress. In those settings, specific immunological functions are heightened to re-enforce processes and tissue sites most critical to survival. Altogether, these examples will emphasize the profound influence nutrition has over the immune system and highlight how a mechanistic exploration of this cross talk could ultimately lead to the design of novel therapeutic approaches that prevent and treat disease.

Keywords:  caloric restriction mimetics; dietary restriction; immunology; microbiota; nutrition; undernutrition

DOI:  https://doi.org/10.1016/j.immuni.2022.01.004