bims-minimp 2022-02-06 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2022–02–06
ten papers selected by
Hanna Salmonowicz, International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.
Targeting regulation of ATP synthase 5 alpha/beta dimerization alleviates senescence.
Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease.
Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria.
Yme2, a putative RNA recognition motif and AAA+ domain containing protein, genetically interacts with the mitochondrial protein export machinery.
The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice.
Mitochondrial- and nuclear genome-controlled bioenergetic gene expression in Alzheimer's disease.
The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.
Endoplasmic reticulum stress induces mitochondrial dysfunction but not mitochondrial unfolded protein response in SH-SY5Y cells.
OTUD7B deubiquitinates SQSTM1/p62 and promotes IRF3 degradation to regulate antiviral immunity.

Nat Commun. 2022 Feb 03. 13(1): 651

Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.

Eirini Lionaki, Ilias Gkikas, Ioanna Daskalaki, Maria-Konstantina Ioannidi, Maria I Klapa, Nektarios Tavernarakis.

Sustained mitochondrial fitness relies on coordinated biogenesis and clearance. Both processes are regulated by constant targeting of proteins into the organelle. Thus, mitochondrial protein import sets the pace for mitochondrial abundance and function. However, our understanding of mitochondrial protein translocation as a regulator of longevity remains enigmatic. Here, we targeted the main protein import translocases and assessed their contribution to mitochondrial abundance and organismal physiology. We find that reduction in cellular mitochondrial load through mitochondrial protein import system suppression, referred to as MitoMISS, elicits a distinct longevity paradigm. We show that MitoMISS triggers the mitochondrial unfolded protein response, orchestrating an adaptive reprogramming of metabolism. Glycolysis and de novo serine biosynthesis are causatively linked to longevity, whilst mitochondrial chaperone induction is dispensable for lifespan extension. Our findings extent the pro-longevity role of UPRmt and provide insight, relevant to the metabolic alterations that promote or undermine survival and longevity.

DOI: https://doi.org/10.1038/s41467-022-28272-1
Aging (Albany NY). 2022 Jan 30. 14(undefined):

Targeting regulation of ATP synthase 5 alpha/beta dimerization alleviates senescence.

Yun Haeng Lee, Doyoung Choi, Geonhee Jang, Ji Yun Park, Eun Seon Song, Haneur Lee, Myeong Uk Kuk, Junghyun Joo, Soon Kil Ahn, Youngjoo Byun, Joon Tae Park.

  Senescence is a distinct set of changes in the senescence-associated secretory phenotype (SASP) and leads to aging and age-related diseases. Here, we screened compounds that could ameliorate senescence and identified an oxazoloquinoline analog (KB1541) designed to inhibit IL-33 signaling pathway. To elucidate the mechanism of action of KB1541, the proteins binding to KB1541 were investigated, and an interaction between KB1541 and 14-3-3ζ protein was found. Specifically, KB1541 interacted with 14-3-3ζ protein and phosphorylated of 14-3-3ζ protein at serine 58 residue. This phosphorylation increased ATP synthase 5 alpha/beta dimerization, which in turn promoted ATP production through increased oxidative phosphorylation (OXPHOS) efficiency. Then, the increased OXPHOS efficiency induced the recovery of mitochondrial function, coupled with senescence alleviation. Taken together, our results demonstrate a mechanism by which senescence is regulated by ATP synthase 5 alpha/beta dimerization upon fine-tuning of KB1541-mediated 14-3-3ζ protein activity.

Keywords:  14–3–3ζ; ATPase synthase 5; KB1541; OXPHOS; senescence amelioration

DOI:  https://doi.org/10.18632/aging.203858
Front Cell Dev Biol. 2021 ;9 796128

Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease.

Alfredo Cabrera-Orefice, Alisa Potter, Felix Evers, Johannes F Hevler, Sergio Guerrero-Castillo.

  Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.

Keywords:  complexome profiling; disease; mass spectrometry; mitochondria; oxidative phosphorylation; protein complex; protein-protein interaction (PPI); proteomics

DOI:  https://doi.org/10.3389/fcell.2021.796128
Genetics. 2022 Jan 20. pii: iyac007. [Epub ahead of print]

Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria.

Anna M Kabala, Krishia Binko, François Godard, Camille Charles, Alain Dautant, Emilia Baranowska, Natalia Skoczen, Kewin Gombeau, Marine Bouhier, Hubert D Becker, Sharon H Ackerman, Lars M Steinmetz, Déborah Tribouillard-Tanvier, Rosa Kucharczyk, Jean-Paul di Rago.

  The yeast mitochondrial ATP synthase is an assembly of 28 subunits of 17 types of which 3 (subunits 6, 8, and 9) are encoded by mitochondrial genes while the 14 others have a nuclear genetic origin. Within the membrane domain (FO) of this enzyme, the subunit 6 and a ring of 10 identical subunits 9 transport protons across the mitochondrial inner membrane coupled to ATP synthesis in the extra-membrane structure (F1) of ATP synthase. As a result of their dual genetic origin, the ATP synthase subunits are synthesized in the cytosol and inside the mitochondrion. How they are produced in the proper stoichiometry from two different cellular compartments is still poorly understood. The experiments herein reported show that the rate of translation of the subunits 9 and 6 is enhanced in strains with mutations leading to specific defects in the assembly of these proteins. These translation modifications involve assembly intermediates interacting with subunits 6 and 9 within the final enzyme and cis-regulatory sequences that control gene expression in the organelle. In addition to enabling a balanced output of the ATP synthase subunits, these assembly-dependent feedback loops are presumably important to limit the accumulation of harmful assembly intermediates that have the potential to dissipate the mitochondrial membrane electrical potential and the main source of chemical energy of the cell.

Keywords:  ATP synthase; Mitochondria; Mitochondria DNA; Mitochondrial biogenesis; Mitochondrial gene expression; yeast

DOI:  https://doi.org/10.1093/genetics/iyac007
Biol Chem. 2022 Jan 31.

Yme2, a putative RNA recognition motif and AAA+ domain containing protein, genetically interacts with the mitochondrial protein export machinery.

Nupur Sharma, Christof Osman.

  The mitochondrial respiratory chain is composed of nuclear as well as mitochondrial-encoded subunits. A variety of factors mediate co-translational integration of mtDNA-encoded proteins into the inner membrane. In Saccharomyces cerevisiae, Mdm38 and Mba1 are ribosome acceptors that recruit the mitochondrial ribosome to the inner membrane, where the insertase Oxa1, facilitates membrane integration of client proteins. The protein Yme2 has previously been shown to be localized in the inner mitochondrial membrane and has been implicated in mitochondrial protein biogenesis, but its mode of action remains unclear. Here, we show that multiple copies of Yme2 assemble into a high molecular weight complex. Using a combination of bioinformatics and mutational analyses, we find that Yme2 possesses an RNA recognition motif (RRM), which faces the mitochondrial matrix and a AAA+ domain that is located in the intermembrane space. We further show that YME2 genetically interacts with MDM38, MBA1 and OXA1, which links the function of Yme2 to the mitochondrial protein biogenesis machinery.

Keywords:  MBA1; MDM38; OXA1; RRM; Walker motifs; mitoribosome

DOI:  https://doi.org/10.1515/hsz-2021-0398
Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2120476119. [Epub ahead of print]119(6):

The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice.

Catherine A Makarewich, Amir Z Munir, Svetlana Bezprozvannaya, Aaron M Gibson, Soo Young Kim, Misty S Martin-Sandoval, Thomas P Mathews, Luke I Szweda, Rhonda Bassel-Duby, Eric N Olson.

  Emerging evidence indicates that a subset of RNA molecules annotated as noncoding contain short open reading frames that code for small functional proteins called microproteins, which have largely been overlooked due to their small size. To search for cardiac-expressed microproteins, we used a comparative genomics approach and identified mitolamban (Mtlbn) as a highly conserved 47-amino acid transmembrane protein that is abundantly expressed in the heart. Mtlbn localizes specifically to the inner mitochondrial membrane where it interacts with subunits of complex III of the electron transport chain and with mitochondrial respiratory supercomplexes. Genetic deletion of Mtlbn in mice altered complex III assembly dynamics and reduced complex III activity. Unbiased metabolomic analysis of heart tissue from Mtlbn knockout mice further revealed an altered metabolite profile consistent with deficiencies in complex III activity. Cardiac-specific Mtlbn overexpression in transgenic (TG) mice induced cardiomyopathy with histological, biochemical, and ultrastructural pathologic features that contributed to premature death. Metabolomic analysis and biochemical studies indicated that hearts from Mtlbn TG mice exhibited increased oxidative stress and mitochondrial dysfunction. These findings reveal Mtlbn as a cardiac-expressed inner mitochondrial membrane microprotein that contributes to mitochondrial electron transport chain activity through direct association with complex III and the regulation of its assembly and function.

Keywords:  cardiac; microprotein; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.1073/pnas.2120476119
Alzheimers Dement. 2021 Dec;17 Suppl 3 e054460

Mitochondrial- and nuclear genome-controlled bioenergetic gene expression in Alzheimer's disease.

Yuan Shang, Fei Yin, Roberta Diaz Brinton.

BACKGROUND: Mitochondrial dysfunction is a hallmark of brain aging and particularly accentuated in neurodegenerative diseases including Alzheimer's disease (AD), yet the regulation of mitochondrial DNA (mtDNA) versus nuclear DNA (nDNA)-encoded genes in the aging- and AD brains is largely unknown.
METHOD: Transcriptome datasets (ROSMAP, Mayo, and MSBB) and proteome dataset (ROSMAP) from cognitively normal and AD brains were analyzed. Linear regression models were applied to evaluate the association between mtDNA-encoded and nDNA-encoded genes at transcript and protein levels. Further, pathway analysis was performed to identify biological processes correlated with mtDNA-encoded gene expression.
RESULT: At transcript level, mtDNA encoded genes were uniformly regulated (average R2 ranging from 0.43 to 0.92) across all datasets analyzed. While mtDNA encoded and nDNA encoded oxidative phosphorylation (OXPHOS) genes were positively correlated at protein level, they were differentially regulated at transcript level. Compared to control brains, both genesets were downregulated in AD brains at protein level whereas at the transcript level, mtDNA transcript number was higher vs nDNA transcript number was lower. In addition, transcriptional correlations between nDNA OXPHOS genes and mtDNA genes were reduced in AD brains. In both normal and AD brains, mtDNA transcripts were consistently correlated with Alzheimer's related pathways, including a positive correlation with notch signaling module and negative correlations with synapse, mitochondrial, translation, and ubiquitin mediated protein clearance modules. Across brain cell types, neuronal cell markers were negatively correlated with mtDNA transcripts whereas markers for oligodendrocyte, astrocyte and endothelial cells exhibited positive correlations.
CONCLUSION: Outcomes of these analyses suggest an underappreciated correlation between mitochondrial gene expression with the development of AD, in particular the coordinated transcriptional regulation across both the mitochondrial- and nuclear genomes. While mitochondria are a promising therapeutic target for Alzheimer's disease, the findings reported herein indicate that restoring optimal mitochondrial function to prevent or treat Alzheimer's remains a complex challenge. This work was supported by National Institute on Aging grants P01-AG026572, R01 AG057931, and R01 AG059093 to RDB.

DOI: https://doi.org/10.1002/alz.054460
Mol Cell. 2022 Jan 28. pii: S1097-2765(22)00008-9. [Epub ahead of print]

The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.

Katia Cosentino, Vanessa Hertlein, Andreas Jenner, Timo Dellmann, Milos Gojkovic, Aida Peña-Blanco, Shashank Dadsena, Noel Wajngarten, John S H Danial, Jervis Vermal Thevathasan, Markus Mund, Jonas Ries, Ana J Garcia-Saez.

  BAX and BAK are key apoptosis regulators that mediate the decisive step of mitochondrial outer membrane permeabilization. However, the mechanism by which they assemble the apoptotic pore remains obscure. Here, we report that BAX and BAK present distinct oligomerization properties, with BAK organizing into smaller structures with faster kinetics than BAX. BAK recruits and accelerates BAX assembly into oligomers that continue to grow during apoptosis. As a result, BAX and BAK regulate each other as they co-assemble into the same apoptotic pores, which we visualize. The relative availability of BAX and BAK molecules thereby determines the growth rate of the apoptotic pore and the relative kinetics by which mitochondrial contents, most notably mtDNA, are released. This feature of BAX and BAK results in distinct activation kinetics of the cGAS/STING pathway with implications for mtDNA-mediated paracrine inflammatory signaling.

Keywords:  AFM; BAK; BAX; BCL-2; inflammatory cell death; membrane pore; mitochondria; pore-forming protein; single-molecule imaging; super-resolution microscopy

DOI:  https://doi.org/10.1016/j.molcel.2022.01.008
Mol Cell Biochem. 2022 Jan 31.

Endoplasmic reticulum stress induces mitochondrial dysfunction but not mitochondrial unfolded protein response in SH-SY5Y cells.

Andrea Evinova, Zuzana Hatokova, Zuzana Tatarkova, Maria Brodnanova, Katarina Dibdiakova, Peter Racay.

  In the present study we have shown that treatment of SH-SY5Y cells with either thapsigargin or tunicamycin is associated with a significant decrease in ROUTINE and ATP-coupled mitochondrial respiration as well as a decrease in spare and maximal respiratory capacity. We have also shown that treating cells with either thapsigargin or tunicamycin is associated with significant changes in mitochondrial membrane potential (ΔΨm) generation, which is mainly associated with the reversal of the succinyl-CoA ligase reaction and a decreased activity of complex II. Despite the induction of endoplasmic reticulum (ER) specific unfolded protein response (UPR), as documented by increased expression of HRD1, ER stress did not induce mitochondrial UPR since the expression of both mitochondrial protease LONP1 and mitochondrial chaperone HSP60 was not significantly altered. Inhibition of IRE1α ribonuclease with STF-083010 did not protect the SH-SY5Y cells from ER stress-induced mitochondrial dysfunction. STF-083010 itself had significant impact on both mitochondrial respiration and generation of ΔΨm, which has mainly been associated with the uncoupling of respiratory chain from ATP synthesis.

Keywords:  Endoplasmic reticulum stress; Mitochondrial dysfunction; Parkinson’s disease; Unfolded protein response

DOI:  https://doi.org/10.1007/s11010-021-04344-6
Autophagy. 2022 Jan 31. 1-15

OTUD7B deubiquitinates SQSTM1/p62 and promotes IRF3 degradation to regulate antiviral immunity.

Weihong Xie, Shuo Tian, Jiahui Yang, Sihui Cai, Shouheng Jin, Tao Zhou, Yaoxing Wu, Zhiyun Chen, Yanqin Ji, Jun Cui.

  Deubiquitination plays an important role in the regulation of the crosstalk between macroautophagy/autophagy and innate immune signaling, yet its regulatory mechanisms are not fully understood. Here we identify the deubiquitinase OTUD7B as a negative regulator of antiviral immunity by targeting IRF3 (interferon regulatory factor 3) for selective autophagic degradation. Mechanistically, OTUD7B interacts with IRF3, and activates IRF3-associated cargo receptor SQSTM1/p62 (sequestosome 1) by removing its K63-linked poly-ubiquitin chains at lysine 7 (K7) to enhance SQSTM1 oligomerization. Moreover, viral infection increased the expression of OTUD7B, which forms a negative feedback loop by promoting IRF3 degradation to balance type I interferon (IFN) signaling. Taken together, our study reveals a specific role of OTUD7B in mediating the activation of cargo receptors in a substrate-dependent manner, which could be a potential target against excessive immune responses.Abbreviations: Baf A1: bafilomycin A1; CGAS: cyclic GMP-AMP synthase; DDX58/RIG-I: DExD/H-box helicase 58; DSS: dextran sodium sulfate; DUBs: deubiquitinating enzymes; GFP: green fluorescent protein; IFN: interferon; IKKi: IKBKB/IkappaB kinase inhibitor; IRF3: interferon regulatory factor 3; ISGs: interferon-stimulated genes; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; PAMPs: pathogen-associated molecular patterns; SeV: Sendai virus; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1; Ub: ubiquitin; WT: wild-type; VSV: vesicular stomatitis virus.

Keywords:  Antiviral immunity; cargo receptor; deubiquitination; selective autophagy; type I interferon signaling

DOI:  https://doi.org/10.1080/15548627.2022.2026098