bims-smemid 2024-07-07 papers

on Stress metabolism in mitochondrial dysfunction

Issue of 2024–07–07
six papers selected by
Deepti Mudartha, The International Institute of Molecular Mechanisms and Machines

Protocol for detecting mitochondria extracellular vesicles of brown adipose tissue in mice.
ATF4-mediated different mode of interaction between autophagy and mTOR determines cell fate dependent on the level of ER stress induced by Cr(VI).
Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly.
Proteolysis and Contractility Regulate Tissue Opening and Wound Healing by Lung Fibroblasts in 3D Microenvironments.
Mitochondrial genetics through the lens of single-cell multi-omics.
Mitochondrial Structure and Function in Human Heart Failure.

STAR Protoc. 2024 Jun 27. pii: S2666-1667(24)00326-5. [Epub ahead of print]5(3): 103161

Protocol for detecting mitochondria extracellular vesicles of brown adipose tissue in mice.

Flavia Tortolici, Claudia Di Biagio, Daniele Lettieri-Barbato, Katia Aquilano.

  Brown adipose tissue (BAT) is mitochondria rich, enabling high oxidative metabolism for non-shivering thermogenesis. The release of large/small extracellular vesicles (EVs) containing mitochondria or mitochondrial fragments, termed mito-EVs, may support mitochondrial quality control or intercellular communication. We present a protocol to isolate and characterize mito-EVs. We detail steps for BAT processing, cell debris removal, differential centrifugation (dC), and mito-EV analysis by flow cytometry and immunoblotting assays. For complete details on the use and execution of this protocol, please refer to Rosina et al.1.

Keywords:  Cell Biology; Cell Membrane; Cell culture; Flow Cytometry; Metabolism; Molecular Biology; Protein Biochemistry

DOI:  https://doi.org/10.1016/j.xpro.2024.103161
Ecotoxicol Environ Saf. 2024 Jul 03. pii: S0147-6513(24)00715-2. [Epub ahead of print]281 116639

ATF4-mediated different mode of interaction between autophagy and mTOR determines cell fate dependent on the level of ER stress induced by Cr(VI).

Xin Zheng, Yuxin Pang, Hasenbilige, Yanqiu Yang, Qiujuan Li, Yong Liu, Jun Cao.

  Hexavalent chromium [Cr(VI)] exists widely in occupational environments. The mechanistic target of rapamycin (mTOR) has been well-documented to regulate autophagy negatively. However, we found that low concentration of Cr(VI) (0.2 μM) elevated both mTOR and autophagy and promote cell survival. Conversely, high concentration of Cr(VI) (6 μM) caused cell death by inhibiting mTOR and subsequently inducing autophagy. Tunicamycin (Tm), as an Endoplasmic reticulum (ER) stress activator was used to induce mild ER stress at 0.1 μg/ml and it activated both autophagy and mTOR, which also caused cell migration in a similar manner to that observed with low concentration of Cr(VI). Severe ER stress caused by Tm (2 μg/ml) decreased mTOR, increased autophagy and then inhibited cell migration, which was the same as 6 μM Cr(VI) treatment, although Cr(VI) in high concentration inhibited ER stress. Activating transcription factor 4 (ATF4), a downstream target of ER stress, only increased under mild ER stress but decreased under severe ER stress and 6 μM Cr(VI) treatment. Chromatin immunoprecipitation (ChIP) experiment indicated that ATF4 could bind to the promoter of ATG4B and AKT1. To sum up, our data revealed that mild ER stress induced by low concentration of Cr(VI) could enhance transcriptional regulation of ATG4B and AKT1 by ATF4, which induced both autophagy and mTOR to promote cell viability.

Keywords:  ATF4; Autophagy; Chromium; ER stress; mTOR

DOI:  https://doi.org/10.1016/j.ecoenv.2024.116639
Nat Struct Mol Biol. 2024 Jul 01.

Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly.

Julian R Braxton, Hao Shao, Eric Tse, Jason E Gestwicki, Daniel R Southworth.

The mitochondrial chaperonin, mitochondrial heat shock protein 60 (mtHsp60), promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin progresses through its ATP-dependent client folding cycle are not clear. Here, we determined cryo-EM structures of a hyperstable disease-associated human mtHsp60 mutant, V72I. Client density is identified in three distinct states, revealing interactions with the mtHsp60 apical domains and C termini that coordinate client positioning in the folding chamber. We further identify an asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60-10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify distinct roles for the apical domains in coordinating client capture and progression through the chaperone cycle, supporting a conserved mechanism of group I chaperonin function.

DOI: https://doi.org/10.1038/s41594-024-01352-0
Adv Healthc Mater. 2024 Jul 05. e2400941

Proteolysis and Contractility Regulate Tissue Opening and Wound Healing by Lung Fibroblasts in 3D Microenvironments.

Hugh Xiao, Kadidia Sylla, Xiangyu Gong, Brendan Wilkowski, Alejandro Rossello-Martinez, Seyma Nayir Jordan, Emmanuel Y Mintah, Allen Zheng, Huanxing Sun, Erica L Herzog, Michael Mak.

  Damage and repair are recurring processes in tissues, with fibroblasts playing key roles by remodeling extracellular matrices (ECM) through protein synthesis, proteolysis, and cell contractility. Dysregulation of fibroblasts can lead to fibrosis and tissue damage, as seen in idiopathic pulmonary fibrosis (IPF). In advanced IPF, tissue damage manifests as honeycombing, or voids in the lungs. This study explores how transforming growth factor-beta (TGF-β), a crucial factor in IPF, induces lung fibroblast spheroids to create voids in reconstituted collagen through proteolysis and cell contractility, a process is termed as hole formation. These voids reduce when proteases are blocked. Spheroids mimic fibroblast foci observed in IPF. Results indicate that cell contractility mediates tissue opening by stretching fractures in the collagen meshwork. Matrix metalloproteinases (MMPs), including MMP1 and MT1-MMP, are essential for hole formation, with invadopodia playing a significant role. Blocking MMPs reduces hole size and promotes wound healing. This study shows how TGF-β induces excessive tissue destruction and how blocking proteolysis can reverse damage, offering insights into IPF pathology and potential therapeutic interventions.

Keywords:  cell mechanics; cell‐matrix interactions; extracellular matrix; fibrosis; matrix metalloproteinases; mechanobiology; tissue remodeling

DOI:  https://doi.org/10.1002/adhm.202400941
Nat Genet. 2024 Jul 01.

Mitochondrial genetics through the lens of single-cell multi-omics.

Lena Nitsch, Caleb A Lareau, Leif S Ludwig.

Mitochondria carry their own genetic information encoding for a subset of protein-coding genes and translational machinery essential for cellular respiration and metabolism. Despite its small size, the mitochondrial genome, its natural genetic variation and molecular phenotypes have been challenging to study using bulk sequencing approaches, due to its variation in cellular copy number, non-Mendelian modes of inheritance and propensity for mutations. Here we highlight emerging strategies designed to capture mitochondrial genetic variation across individual cells for lineage tracing and studying mitochondrial genetics in primary human cells and clinical specimens. We review recent advances surrounding single-cell mitochondrial genome sequencing and its integration with functional genomic readouts, including leveraging somatic mitochondrial DNA mutations as clonal markers that can resolve cellular population dynamics in complex human tissues. Finally, we discuss how single-cell whole mitochondrial genome sequencing approaches can be utilized to investigate mitochondrial genetics and its contribution to cellular heterogeneity and disease.

DOI: https://doi.org/10.1038/s41588-024-01794-8
Circ Res. 2024 Jul 05. 135(2): 372-396

Mitochondrial Structure and Function in Human Heart Failure.

Antentor Hinton, Steven M Claypool, Kit Neikirk, Nanami Senoo, Celestine N Wanjalla, Annet Kirabo, Clintoria R Williams.

  Despite clinical and scientific advancements, heart failure is the major cause of morbidity and mortality worldwide. Both mitochondrial dysfunction and inflammation contribute to the development and progression of heart failure. Although inflammation is crucial to reparative healing following acute cardiomyocyte injury, chronic inflammation damages the heart, impairs function, and decreases cardiac output. Mitochondria, which comprise one third of cardiomyocyte volume, may prove a potential therapeutic target for heart failure. Known primarily for energy production, mitochondria are also involved in other processes including calcium homeostasis and the regulation of cellular apoptosis. Mitochondrial function is closely related to morphology, which alters through mitochondrial dynamics, thus ensuring that the energy needs of the cell are met. However, in heart failure, changes in substrate use lead to mitochondrial dysfunction and impaired myocyte function. This review discusses mitochondrial and cristae dynamics, including the role of the mitochondria contact site and cristae organizing system complex in mitochondrial ultrastructure changes. Additionally, this review covers the role of mitochondria-endoplasmic reticulum contact sites, mitochondrial communication via nanotunnels, and altered metabolite production during heart failure. We highlight these often-neglected factors and promising clinical mitochondrial targets for heart failure.

Keywords:  cardiovascular diseases; heart failure; hypertension; mitochondria; myocardium

DOI:  https://doi.org/10.1161/CIRCRESAHA.124.323800