bims-apauto 2023-01-22 papers

bims-apauto

Biomed News

on Apoptosis and autophagy

Issue of 2023–01–22
seven papers selected by
Su Hyun Lee, Harvard University

ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy.
The role of autophagy in viral infections.
Control of Mitochondrial Activity by the Ubiquitin Code in Health and Cancer.
From seeds to trees: how E2 enzymes grow ubiquitin chains.
Balanced activities of Hsp70 and the ubiquitin proteasome system underlie cellular protein homeostasis.
Organelle-Specific Mechanisms in Crosstalk between Apoptosis and Ferroptosis.
Site-specific ubiquitination of VDAC1 restricts its oligomerization and mitochondrial DNA release in liver fibrosis.

J Cell Sci. 2023 Jan 16. pii: jcs.260546. [Epub ahead of print]

ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy.

Pablo Sánchez-Martín, Franziska Kriegenburg, Ludovico Alves, Julius Adam, Jana Elsaesser, Riccardo Babic, Hector Mancilla, Mariya Licheva, Georg Tascher, Christian Münch, Stefan Eimer, Claudine Kraft.

  Autophagy is a catabolic process during which cytosolic material is enwrapped in a newly formed double membrane structure called the autophagosome, and subsequently targeted for degradation in the lytic compartment of the cell. The fusion of autophagosomes with the lytic compartment is a tightly regulated step and involves membrane-bound SNARE proteins. These play a crucial role as they promote lipid mixing and fusion of the opposing membranes. Among the SNARE proteins implicated in autophagy, the essential SNARE protein YKT6 is the only SNARE protein evolutionary conserved from yeast to humans. Here we show that alterations in YKT6 function, in both mammalian cells and nematodes, produce early and late autophagy defects that result in reduced survival. Moreover, mammalian autophagosomal YKT6 is phospho-regulated by the ULK1 kinase, preventing premature bundling with the lysosomal SNARE proteins and thereby inhibiting autophagosome-lysosome fusion. Together, our findings reveal that timely regulation of the YKT6 phosphorylation status is crucial throughout autophagy progression and cell survival.

Keywords:  ULK1; autophagosome; autophagy; SNARE; YKT6

DOI:  https://doi.org/10.1242/jcs.260546
J Biomed Sci. 2023 Jan 18. 30(1): 5

The role of autophagy in viral infections.

Tong Chen, Shaoyu Tu, Ling Ding, Meilin Jin, Huanchun Chen, Hongbo Zhou.

  Autophagy is an evolutionarily conserved catabolic cellular process that exerts antiviral functions during a viral invasion. However, co-evolution and co-adaptation between viruses and autophagy have armed viruses with multiple strategies to subvert the autophagic machinery and counteract cellular antiviral responses. Specifically, the host cell quickly initiates the autophagy to degrade virus particles or virus components upon a viral infection, while cooperating with anti-viral interferon response to inhibit the virus replication. Degraded virus-derived antigens can be presented to T lymphocytes to orchestrate the adaptive immune response. Nevertheless, some viruses have evolved the ability to inhibit autophagy in order to evade degradation and immune responses. Others induce autophagy, but then hijack autophagosomes as a replication site, or hijack the secretion autophagy pathway to promote maturation and egress of virus particles, thereby increasing replication and transmission efficiency. Interestingly, different viruses have unique strategies to counteract different types of selective autophagy, such as exploiting autophagy to regulate organelle degradation, metabolic processes, and immune responses. In short, this review focuses on the interaction between autophagy and viruses, explaining how autophagy serves multiple roles in viral infection, with either proviral or antiviral functions.

Keywords:  Autophagy degradation; Immune response; Selective autophagy; Viral infection; Viral replication

DOI:  https://doi.org/10.1186/s12929-023-00899-2
Cells. 2023 Jan 05. pii: 234. [Epub ahead of print]12(2):

Control of Mitochondrial Activity by the Ubiquitin Code in Health and Cancer.

Laura Rinaldi, Emanuela Senatore, Rosa Iannucci, Francesco Chiuso, Antonio Feliciello.

  Cellular homeostasis is tightly connected to the broad variety of mitochondrial functions. To stay healthy, cells need a constant supply of nutrients, energy production and antioxidants defenses, undergoing programmed death when a serious, irreversible damage occurs. The key element of a functional integration of all these processes is the correct crosstalk between cell signaling and mitochondrial activities. Once this crosstalk is interrupted, the cell is not able to communicate its needs to mitochondria, resulting in oxidative stress and development of pathological conditions. Conversely, dysfunctional mitochondria may affect cell viability, even in the presence of nutrients supply and energy production, indicating the existence of feed-back control mechanisms between mitochondria and other cellular compartments. The ubiquitin proteasome system (UPS) is a multi-step biochemical pathway that, through the conjugation of ubiquitin moieties to specific protein substrates, controls cellular proteostasis and signaling, removing damaged or aged proteins that might otherwise accumulate and affect cell viability. In response to specific needs or changed extracellular microenvironment, the UPS modulates the turnover of mitochondrial proteins, thus influencing the organelle shape, dynamics and function. Alterations of the dynamic and reciprocal regulation between mitochondria and UPS underpin genetic and proliferative disorders. This review focuses on the mitochondrial metabolism and activities supervised by UPS and examines how deregulation of this control mechanism results in proliferative disorders and cancer.

Keywords:  UPS; cancer; dynamics; metabolism; mitochondria

DOI:  https://doi.org/10.3390/cells12020234
Biochem Soc Trans. 2023 Jan 16. pii: BST20220880. [Epub ahead of print]

From seeds to trees: how E2 enzymes grow ubiquitin chains.

Adam J Middleton, Catherine L Day.

  Modification of proteins by ubiquitin is a highly regulated process that plays a critical role in eukaryotes, from the construction of signalling platforms to the control of cell division. Aberrations in ubiquitin transfer are associated with many diseases, including cancer and neurodegenerative disorders. The ubiquitin machinery generates a rich code on substrate proteins, spanning from single ubiquitin modifications to polyubiquitin chains with diverse linkage types. Central to this process are the E2 enzymes, which often determine the exact nature of the ubiquitin code. The focus of this mini-review is on the molecular details of how E2 enzymes can initiate and grow ubiquitin chains. In particular, recent developments and biochemical breakthroughs that help explain how the degradative E2 enzymes, Ube2s, Ube2k, and Ube2r, generate complex ubiquitin chains with exquisite specificity will be discussed.

Keywords:  E2 enzymes; protein degradation; ubiquitin; ubiquitin chains; ubiquitin signalling

DOI:  https://doi.org/10.1042/BST20220880
Front Mol Biosci. 2022 ;9 1106477

Balanced activities of Hsp70 and the ubiquitin proteasome system underlie cellular protein homeostasis.

Areeb Jawed, Chi-Ting Ho, Tomas Grousl, Aseem Shrivastava, Thomas Ruppert, Bernd Bukau, Axel Mogk.

  To counteract proteotoxic stress and cellular aging, protein quality control (PQC) systems rely on the refolding, degradation and sequestration of misfolded proteins. In Saccharomyces cerevisiae the Hsp70 chaperone system plays a central role in protein refolding, while degradation is predominantly executed by the ubiquitin proteasome system (UPS). The sequestrases Hsp42 and Btn2 deposit misfolded proteins in cytosolic and nuclear inclusions, thereby restricting the accessibility of misfolded proteins to Hsp70 and preventing the exhaustion of limited Hsp70 resources. Therefore, in yeast, sequestrase mutants show negative genetic interactions with double mutants lacking the Hsp70 co-chaperone Fes1 and the Hsp104 disaggregase (fes1Δ hsp104Δ, ΔΔ) and suffering from low Hsp70 capacity. Growth of ΔΔbtn2Δ mutants is highly temperature-sensitive and results in proteostasis breakdown at non-permissive temperatures. Here, we probed for the role of the ubiquitin proteasome system in maintaining protein homeostasis in ΔΔbtn2Δ cells, which are affected in two major protein quality control branches. We show that ΔΔbtn2Δ cells induce expression of diverse stress-related pathways including the ubiquitin proteasome system to counteract the proteostasis defects. Ubiquitin proteasome system dependent degradation of the stringent Hsp70 substrate firefly Luciferase in the mutant cells mirrors such compensatory activities of the protein quality control system. Surprisingly however, the enhanced ubiquitin proteasome system activity does not improve but aggravates the growth defects of ΔΔbtn2Δ cells. Reducing ubiquitin proteasome system activity in the mutant by lowering the levels of functional 26S proteasomes improved growth, increased refolding yield of the Luciferase reporter and attenuated global stress responses. Our findings indicate that an imbalance between Hsp70-dependent refolding, sequestration and ubiquitin proteasome system-mediated degradation activities strongly affects protein homeostasis of Hsp70 capacity mutants and contributes to their severe growth phenotypes.

Keywords:  26S proteasome; Hsp70; chaperone; protein quality control; protein sequestration

DOI:  https://doi.org/10.3389/fmolb.2022.1106477
Oxid Med Cell Longev. 2023 ;2023 3400147

Organelle-Specific Mechanisms in Crosstalk between Apoptosis and Ferroptosis.

Peiyao Wu, Xiaoyue Zhang, Dingyu Duan, Lei Zhao.

Apoptosis has been extensively studied, whereas ferroptosis is a newly discovered form of regulated cell death that involves iron-dependent accumulations of lipid hydroperoxides. While these two cell death mechanisms were initially believed to be mutually exclusive, recent studies have revealed cellular contexts requiring a balanced interaction between them. Numerous subcellular sites and signaling molecules within these sites are involved in both processes, either as modules or switches that allow cells to choose on how to proceed. The close relationships between apoptosis and ferroptosis, as well as the possibility of switching from one to the other, are described in this review. To understand the crosstalk between apoptosis and ferroptosis, various organelle-specific mechanisms must be analyzed and compared. The ability to switch apoptosis to ferroptosis by targeting cellular organelles has a great potential in cancer therapy.

DOI: https://doi.org/10.1155/2023/3400147
Exp Mol Med. 2023 Jan 19.

Site-specific ubiquitination of VDAC1 restricts its oligomerization and mitochondrial DNA release in liver fibrosis.

Ne N Wu, Lifeng Wang, Lu Wang, Xihui Xu, Gary D Lopaschuk, Yingmei Zhang, Jun Ren.

Mitochondrial DNA (mtDNA) released through protein oligomers, such as voltage-dependent anion channel 1 (VDAC1), triggers innate immune activation and thus contributes to liver fibrosis. Here, we investigated the role of Parkin, an important regulator of mitochondria, and its regulation of VDAC1-mediated mtDNA release in liver fibrosis. The circulating mitochondrial DNA (mtDNA) and protein levels of liver Parkin and VDAC1 were upregulated in patients with liver fibrosis. A 4-week CCl4 challenge induced release of mtDNA, activation of STING signaling, a decline in autophagy, and apoptosis in mouse livers, and the knockout of Parkin aggravated these effects. In addition, Parkin reduced mtDNA release and prevented VDAC1 oligomerization in a manner dependent on its E3 activity in hepatocytes. We found that site-specific ubiquitination of VDAC1 at lysine 53 by Parkin interrupted VDAC1 oligomerization and prevented mtDNA release into the cytoplasm under stress. The ubiquitination-defective VDAC1 K53R mutant predominantly formed oligomers that resisted suppression by Parkin. Hepatocytes expressing VDAC1 K53R exhibited mtDNA release and thus activated the STING signaling pathway in hepatic stellate cells, and this effect could not be abolished by Parkin. We propose that the ubiquitination of VDAC1 at a specific site by Parkin confers protection against liver fibrosis by interrupting VDAC1 oligomerization and mtDNA release.

DOI: https://doi.org/10.1038/s12276-022-00923-9