bims-smemid 2024-05-26 papers

on Stress metabolism in mitochondrial dysfunction

Issue of 2024–05–26
eight papers selected by
Deepti Mudartha, The International Institute of Molecular Mechanisms and Machines

Illuminating mitochondrial translation through mouse models.
Coordinating mitochondrial translation with assembly of the OXPHOS complexes.
Lipidomics reveals the reshaping of the mitochondrial phospholipid profile in cells lacking OPA1 and Mitofusins.
Central dogma rates in human mitochondria.
The molecular machinery for maturation of primary mtDNA transcripts.
Leucyl-tRNA synthetase contributes to muscle weakness through mTORC1 activation and autophagy suppression in a mouse model of Duchenne Muscular Dystrophy.
TFAM is an autophagy receptor that limits inflammation by binding to cytoplasmic mitochondrial DNA.
Emerging functions of the mitochondria-ER-lipid droplet three-way junction in coordinating lipid transfer, metabolism, and storage in cells.

Hum Mol Genet. 2024 May 22. 33(R1): R61-R79

Illuminating mitochondrial translation through mouse models.

Laetitia A Hughes, Oliver Rackham, Aleksandra Filipovska.

  Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.

Keywords:  animal models; gene expression; mitochondria; protein synthesis

DOI:  https://doi.org/10.1093/hmg/ddae020
Hum Mol Genet. 2024 May 22. 33(R1): R47-R52

Coordinating mitochondrial translation with assembly of the OXPHOS complexes.

Laura S Kremer, Peter Rehling.

  The mitochondrial oxidative phosphorylation (OXPHOS) system produces the majority of energy required by cells. Given the mitochondrion's endosymbiotic origin, the OXPHOS machinery is still under dual genetic control where most OXPHOS subunits are encoded by the nuclear DNA and imported into mitochondria, while a small subset is encoded on the mitochondrion's own genome, the mitochondrial DNA (mtDNA). The nuclear and mtDNA encoded subunits must be expressed and assembled in a highly orchestrated fashion to form a functional OXPHOS system and meanwhile prevent the generation of any harmful assembly intermediates. While several mechanisms have evolved in eukaryotes to achieve such a coordinated expression, this review will focus on how the translation of mtDNA encoded OXPHOS subunits is tailored to OXPHOS assembly.

Keywords:  Coordination of translation and assembly; Gene expression; Mitochondria; OXPHOS assembly; Oxidative phosphorylation (OXPHOS); Translation

DOI:  https://doi.org/10.1093/hmg/ddae025
J Lipid Res. 2024 May 17. pii: S0022-2275(24)00068-3. [Epub ahead of print] 100563

Lipidomics reveals the reshaping of the mitochondrial phospholipid profile in cells lacking OPA1 and Mitofusins.

Andrea Castellaneta, Ilario Losito, Vito Porcelli, Serena Barile, Alessandra Maresca, Valentina Del Dotto, Valentina Losacco, Ludovica Sofia Guadalupi, Cosima Damiana Calvano, David C Chan, Valerio Carelli, Luigi Palmieri, Tommaso R I Cataldi.

  Depletion or mutations of key proteins for mitochondrial fusion, like optic atrophy 1 (OPA1) and Mitofusins 1 and 2 (Mfn 1 and 2), are known to significantly impact the mitochondrial ultrastructure, suggesting alterations of their membranes' lipid profiles. In order to make an insight into this issue, we used hydrophilic interaction liquid chromatography (HILIC) coupled with electrospray ionization-high resolution mass spectrometry to investigate the mitochondrial phospholipid (PL) profile of mouse embryonic fibroblasts (MEFs) knocked out for OPA1 and Mfn1/2 genes. 167 different sum compositions were recognized for the four major PL classes of mitochondria, namely phosphatidylcholines (PC, 63), phosphatidylethanolamines (PE, 55), phosphatidylinositols (PI, 21) and cardiolipins (CL, 28). A slight decrease in the CL/PC ratio was found for Mfn1/2-knock out mitochondria. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were subsequently used to further process HILIC-ESI-MS data. A progressive decrease in the incidence of alk(en)yl/acyl species in PC and PE classes and a general increase in the incidence of unsaturated acyl chains across all the investigated PL classes was inferred in OPA1 and Mfn1/2 knockouts compared to wild-type MEFs. These findings suggest a reshaping of the PL profile consistent with the changes observed in the mitochondrial ultrastructure when fusion proteins are absent. Based on the existing knowledge on the metabolism of mitochondrial phospholipids, we propose that fusion proteins, especially mitofusins, might influence the PL transfer between the mitochondria and the endoplasmic reticulum, likely in the context of mitochondria-associated membranes (MAMs).

Keywords:  OPA1; glycerophospholipids; high resolution mass spectrometry; hydrophilic interaction liquid chromatography; lipidomics; mitochondria; mitofusins; mouse embryonic fibroblasts; phospholipids; phospholipids/biosynthesis

DOI:  https://doi.org/10.1016/j.jlr.2024.100563
Hum Mol Genet. 2024 May 22. 33(R1): R34-R41

Central dogma rates in human mitochondria.

Erik McShane, L Stirling Churchman.

  In human cells, the nuclear and mitochondrial genomes engage in a complex interplay to produce dual-encoded oxidative phosphorylation (OXPHOS) complexes. The coordination of these dynamic gene expression processes is essential for producing matched amounts of OXPHOS protein subunits. This review focuses on our current understanding of the mitochondrial central dogma rates, highlighting the striking differences in gene expression rates between mitochondrial and nuclear genes. We synthesize a coherent model of mitochondrial gene expression kinetics, highlighting the emerging principles and emphasizing where more precise measurements would be beneficial. Such an understanding is pivotal for grasping the unique aspects of mitochondrial function and its role in cellular energetics, and it has profound implications for aging, metabolic disorders, and neurodegenerative diseases.

Keywords:  gene regulation; mitochondrial DNA; mitonuclear balance; oxidative phosphorylation

DOI:  https://doi.org/10.1093/hmg/ddae036
Hum Mol Genet. 2024 May 22. 33(R1): R19-R25

The molecular machinery for maturation of primary mtDNA transcripts.

Ana Vučković, Christoph Freyer, Anna Wredenberg, Hauke S Hillen.

  Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.

Keywords:  Mitochondria; Mitochondriopathy; RNA; RNA Processing

DOI:  https://doi.org/10.1093/hmg/ddae023
Am J Pathol. 2024 May 16. pii: S0002-9440(24)00174-3. [Epub ahead of print]

Leucyl-tRNA synthetase contributes to muscle weakness through mTORC1 activation and autophagy suppression in a mouse model of Duchenne Muscular Dystrophy.

Jae-Sung You, Kate Karaman, Adriana Reyes-Ordoñez, Soohyun Lee, Yongdeok Kim, Rashid Bashir, Jie Chen.

  Duchenne muscular dystrophy (DMD), caused by loss-of-function mutations in the dystrophin gene, results in progressive muscle weakness and early fatality. Impaired autophagy is one of the cellular hallmarks of DMD, contributing to the disease progression. Molecular mechanisms underlying the inhibition of autophagy in DMD are not well understood. In the current study the DMD mouse model mdx is used for the investigation of signaling pathways leading to suppression of autophagy. Mammalian target of rapamycin complex 1 (mTORC1) is found to be hyperactive in the DMD muscles, accompanying muscle weakness and autophagy impairment. Surprisingly, Akt, a well-known upstream regulator of mTORC1, is not responsible for mTORC1 activation or the dystrophic muscle phenotypes. Instead, leucyl-tRNA synthetase (LeuRS) is found to be overexpressed in mdx muscles compared to the wild-type. LeuRS is known to activate mTORC1 in a non-canonical mechanism that involves interaction with RagD, an activator of mTORC1. Disrupting LeuRS interaction with RagD by the small-molecule inhibitor BC-LI-0186 reduces mTORC1 activity, restores autophagy, and ameliorates myofiber damage in the mdx muscles. Furthermore, inhibition of LeuRS by BC-LI-0186 improves dystrophic muscle strength in an autophagy-dependent manner. Taken together, our findings uncover a non-canonical function of the house-keeping protein LeuRS as a potential therapeutic target in the treatment of DMD.

Keywords:  Duchenne Muscular Dystrophy; autophagy; leucyl-tRNA synthetase; mTORC1; skeletal muscle weakness

DOI:  https://doi.org/10.1016/j.ajpath.2024.04.006
Nat Cell Biol. 2024 May 23.

TFAM is an autophagy receptor that limits inflammation by binding to cytoplasmic mitochondrial DNA.

Hao Liu, Cien Zhen, Jianming Xie, Zhenhuan Luo, Lin Zeng, Guojun Zhao, Shaohua Lu, Haixia Zhuang, Hualin Fan, Xia Li, Zhaojie Liu, Shiyin Lin, Huilin Jiang, Yuqian Chen, Jiahao Cheng, Zhiyu Cao, Keyu Dai, Jinhua Shi, Zhaohua Wang, Yongquan Hu, Tian Meng, Chuchu Zhou, Zhiyuan Han, Huansen Huang, Qinghua Zhou, Pengcheng He, Du Feng.

When cells are stressed, DNA from energy-producing mitochondria can leak out and drive inflammatory immune responses if not cleared. Cells employ a quality control system called autophagy to specifically degrade damaged components. We discovered that mitochondrial transcription factor A (TFAM)-a protein that binds mitochondrial DNA (mtDNA)-helps to eliminate leaked mtDNA by interacting with the autophagy protein LC3 through an autolysosomal pathway (we term this nucleoid-phagy). TFAM contains a molecular zip code called the LC3 interacting region (LIR) motif that enables this binding. Although mutating TFAM's LIR motif did not affect its normal mitochondrial functions, more mtDNA accumulated in the cell cytoplasm, activating inflammatory signalling pathways. Thus, TFAM mediates autophagic removal of leaked mtDNA to restrict inflammation. Identifying this mechanism advances understanding of how cells exploit autophagy machinery to selectively target and degrade inflammatory mtDNA. These findings could inform research on diseases involving mitochondrial damage and inflammation.

DOI: https://doi.org/10.1038/s41556-024-01419-6
FEBS Lett. 2024 May;598(10): 1252-1273

Emerging functions of the mitochondria-ER-lipid droplet three-way junction in coordinating lipid transfer, metabolism, and storage in cells.

Vera Filipa Monteiro-Cardoso, Francesca Giordano.

  Over the past two decades, we have witnessed a growing appreciation for the importance of membrane contact sites (CS) in facilitating direct communication between organelles. CS are tiny regions where the membranes of two organelles meet but do not fuse and allow the transfer of metabolites between organelles, playing crucial roles in the coordination of cellular metabolic activities. The significant advancements in imaging techniques and molecular and cell biology research have revealed that CS are more complex than what originally thought, and as they are extremely dynamic, they can remodel their shape, composition, and functions in accordance with metabolic and environmental changes and can occur between more than two organelles. Here, we describe how recent studies led to the identification of a three-way mitochondria-ER-lipid droplet CS and discuss the emerging functions of these contacts in maintaining lipid storage, homeostasis, and balance. We also summarize the properties and functions of key protein components localized at the mitochondria-ER-lipid droplet interface, with a special focus on lipid transfer proteins. Understanding tripartite CS is essential for unraveling the complexities of inter-organelle communication and cooperation within cells.

Keywords:  MAM; contact sites; fatty acids; lipid metabolism; lipid transfer proteins

DOI:  https://doi.org/10.1002/1873-3468.14893