1
|
Xie Z, Chai Y, Zhu Z, Shen Z, Guo Z, Zhao Z, Xiao L, Du Z, Ou G, Li W. Vacuolar H +-ATPase determines daughter cell fates through asymmetric segregation of the nucleosome remodeling and deacetylase complex. eLife 2024; 12:RP89032. [PMID: 38994733 PMCID: PMC11245309 DOI: 10.7554/elife.89032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
Asymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates through epigenetic mechanisms. However, the process of partitioning different epigenetic information into daughter cells remains unclear. Here, we demonstrate that the nucleosome remodeling and deacetylase (NuRD) complex is asymmetrically segregated into the surviving daughter cell rather than the apoptotic one during ACDs in Caenorhabditis elegans. The absence of NuRD triggers apoptosis via the EGL-1-CED-9-CED-4-CED-3 pathway, while an ectopic gain of NuRD enables apoptotic daughter cells to survive. We identify the vacuolar H+-adenosine triphosphatase (V-ATPase) complex as a crucial regulator of NuRD's asymmetric segregation. V-ATPase interacts with NuRD and is asymmetrically segregated into the surviving daughter cell. Inhibition of V-ATPase disrupts cytosolic pH asymmetry and NuRD asymmetry. We suggest that asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates.
Collapse
Affiliation(s)
- Zhongyun Xie
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Yongping Chai
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Zhiwen Zhu
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Zijie Shen
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Zhengyang Guo
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Zhiguang Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijingChina
| | - Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijingChina
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Chinese Academy of SciencesBeijingChina
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua UniversityBeijingChina
| | - Wei Li
- School of Medicine, Tsinghua UniversityBeijingChina
| |
Collapse
|
2
|
Sánchez-Martín P, Kriegenburg F, Alves L, Adam J, Elsaesser J, Babic R, Mancilla H, Licheva M, Tascher G, Münch C, Eimer S, Kraft C. ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy. J Cell Sci 2023; 136:jcs260546. [PMID: 36644903 PMCID: PMC10022743 DOI: 10.1242/jcs.260546] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
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 that is evolutionarily 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.
Collapse
Affiliation(s)
- Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Ludovico Alves
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Julius Adam
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Jana Elsaesser
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Riccardo Babic
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hector Mancilla
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt, Germany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
3
|
Ploumi C, Sotiriou A, Tavernarakis N. Monitoring autophagic flux in Caenorhabditis elegans using a p62/SQST-1 reporter. Methods Cell Biol 2020; 165:73-87. [PMID: 34311872 DOI: 10.1016/bs.mcb.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Autophagy is a well-conserved self-degrading mechanism, which involves the elimination of unnecessary or damaged cellular constituents. Although extensively studied, many aspects regarding its tight regulation and its implication in health and disease remain elusive. The nematode Caenorhabditis elegans has been widely used as a simple multicellular model organism for studying the autophagic machinery per se, and uncover its multidimensional roles in the maintenance of cellular and organismal homeostasis. The current protocol describes the in vivo detection and biochemical analysis of the autophagic substrate SQST-1, as an indicator of autophagic flux in C. elegans.
Collapse
Affiliation(s)
- Christina Ploumi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Aggeliki Sotiriou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Crete, Greece.
| |
Collapse
|
4
|
Wang Q, Zhou Y, Fu R, Zhu Y, Song B, Zhong Y, Wu S, Shi Y, Wu Y, Su Y, Zhang H, He Y. Distinct autophagy-inducing abilities of similar-sized nanoparticles in cell culture and live C. elegans. NANOSCALE 2018; 10:23059-23069. [PMID: 30511716 DOI: 10.1039/c8nr05851b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanomaterial-induced autophagy has raised increasing concerns. A variety of nanomaterials, conventional or recently emerged, have the capability of inducing autophagy. As a consequence, it is becoming a popular belief that induction of autophagy is a common response of cells upon exposure to nanoscale materials. In order to clarify whether the "nanoscale" size is the determining factor for the nanomaterials to induce autophagy, we utilized in vitro cultured cells and an in vivo Caenorhabditis elegans (C. elegans) model to systemically investigate the autophagy-inducing ability of nanomaterials. We selected four types of representative nanomaterials with similar sizes, namely silicon nanoparticles (SiNPs), CdTe quantum dots (QDs), carbon dots (CDs) and gold nanoparticles (AuNPs). We demonstrated that, unlike most other nanomaterials tested, no autophagosome formation was detected in cultured cells or in live C. elegans with SiNP treatment. The expression of autophagy-related genes and the lipidation of LGG-1/LC3 in cells and C. elegans also remained unchanged after the treatment of SiNPs. In addition, the ability of the nanomaterials to induce autophagy appeared to correlate with those to incur subcellular organelle damage. Together, our studies demonstrate that SiNPs do not induce autophagy in vitro or in vivo in the selected model organisms and cell lines, thus clarifying that the "nanoscale" size is not the determining factor for the nanomaterials to induce autophagy. The results also suggest that the autophagy-inducing ability of most nanomaterials could be merely a reflection of their detrimental effect on cellular structures.
Collapse
Affiliation(s)
- Qin Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences (IBMS), Soochow University, Suzhou, Jiangsu 215123, China.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Approaches for Studying Autophagy in Caenorhabditis elegans. Cells 2017; 6:cells6030027. [PMID: 28867808 PMCID: PMC5617973 DOI: 10.3390/cells6030027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/25/2017] [Accepted: 08/26/2017] [Indexed: 01/10/2023] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is an intracellular degradative process, well conserved among eukaryotes. By engulfing cytoplasmic constituents into the autophagosome for degradation, this process is involved in the maintenance of cellular homeostasis. Autophagy induction triggers the formation of a cup-shaped double membrane structure, the phagophore, which progressively elongates and encloses materials to be removed. This double membrane vesicle, which is called an autophagosome, fuses with lysosome and forms the autolysosome. The inner membrane of the autophagosome, along with engulfed compounds, are degraded by lysosomal enzymes, which enables the recycling of carbohydrates, amino acids, nucleotides, and lipids. In response to various factors, autophagy can be induced for non-selective degradation of bulk cytoplasm. Autophagy is also able to selectively target cargoes and organelles such as mitochondria or peroxisome, functioning as a quality control system. The modification of autophagy flux is involved in developmental processes such as resistance to stress conditions, aging, cell death, and multiple pathologies. So, the use of animal models is essential for understanding these processes in the context of different cell types throughout the entire lifespan. For almost 15 years, the nematode Caenorhabditis elegans has emerged as a powerful model to analyze autophagy in physiological or pathological contexts. This review presents a rapid overview of physiological processes involving autophagy in Caenorhabditis elegans, the different assays used to monitor autophagy, their drawbacks, and specific tools for the analyses of selective autophagy.
Collapse
|