bims-lypmec 2024-11-03 papers

Issue of 2024‒11‒03
five papers selected by
Satoru Kobayashi, New York Institute of Technology

Dev Cell. 2024 Oct 21. pii: S1534-5807(24)00604-X. [Epub ahead of print]

An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity.

Roni Levin-Konigsberg, Koushambi Mitra, Kaitlyn Spees, AkshatKumar Nigam, Katherine Liu, Camille Januel, Pravin Hivare, Sophia M Arana, Laura M Prolo, Anshul Kundaje, Manuel D Leonetti, Yamuna Krishnan, Michael C Bassik.

Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity cause ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH4+). Ammonium buildup compromises lysosomal function, suggesting the existence of mechanisms that protect cells from ammonium toxicity. Here, we identified SLC12A9 as a lysosomal-resident protein that preserves organelle homeostasis by controlling ammonium and chloride levels. SLC12A9 knockout (KO) cells showed grossly enlarged lysosomes and elevated ammonium content. These phenotypes were reversed upon removal of the metabolic source of ammonium or dissipation of the lysosomal pH gradient. Lysosomal chloride increased in SLC12A9 KO cells, and chloride binding by SLC12A9 was required for ammonium transport. Our data indicate that SLC12A9 function is central for the handling of lysosomal ammonium and chloride, an unappreciated, fundamental mechanism of lysosomal physiology that may have special relevance in tissues with elevated ammonia, such as tumors.

Keywords: SLC12A9; ammonium; chloride; ion transport; lysosome metabolism; lysosome volume regulation

DOI: https://doi.org/10.1016/j.devcel.2024.10.003

Int J Mol Sci. 2024 Oct 17. pii: 11160. [Epub ahead of print]25(20):

The Knowns and Unknowns of Membrane Features and Changes During Autophagosome-Lysosome/Vacuole Fusion.

Jinmeng Liu, Hanyu Ma, Zulin Wu, Yanling Ji, Yongheng Liang.

Autophagosome (AP)-lysosome/vacuole fusion is one of the hallmarks of macroautophagy. Membrane features and changes during the fusion process have mostly been described using two-dimensional (2D) models with one AP and one lysosome/vacuole. The outer membrane (OM) of a closed mature AP has been suggested to fuse with the lysosomal/vacuolar membrane. However, the descriptions in some studies for fusion-related issues are questionable or incomplete. The correct membrane features of APs and lysosomes/vacuoles are the prerequisite for describing the fusion process. We searched the literature for representative membrane features of AP-related structures based on electron microscopy (EM) graphs of both animal and yeast cells and re-evaluated the findings. We also summarized the main 2D models describing the membrane changes during AP-lysosome/vacuole fusion in the literature. We used three-dimensional (3D) models to characterize the known and unknown membrane changes during and after fusion of the most plausible 2D models. The actual situation is more complex, since multiple lysosomes may fuse with the same AP in mammalian cells, multiple APs may fuse with the same vacuole in yeast cells, and in some mutant cells, phagophores (unclosed APs) fuse with lysosomes/vacuoles. This review discusses the membrane features and highly dynamic changes during AP (phagophore)-lysosome/vacuole fusion. The resulting information will improve the understanding of AP-lysosome/vacuole fusion and direct the future research on AP-lysosome/vacuole fusion and regeneration.

Keywords: 2D models; 3D models; autophagic body; autophagosome; autophagosome–lysosome/vacuole fusion; double membrane; electron microscopy; lysosome; single membrane; vacuole

DOI: https://doi.org/10.3390/ijms252011160

Korean J Physiol Pharmacol. 2024 Nov 01. 28(6): 495-501

Precision proteomics with TurboID: mapping the suborganelle landscape.

Han Byeol Kim, Kwang-Eun Kim.

Recent research underscores the pivotal role of cellular organelles, such as mitochondria, the endoplasmic reticulum, and lysosomes, in maintaining cellular homeostasis. Their dynamic interactions are critical for metabolic regulation and stress response. Analysis of organelle proteomes offers valuable insights into their functions in both physiology and disease. Traditional proteomic approaches to studying isolated organelles are now complemented by innovative methodologies focusing on inter-organelle interactions. This review examines the integration of advanced proximity labeling technologies, including TurboID and split-TurboID, which address the inherent limitations of traditional techniques and enable precision proteomics of suborganelle compartments and inter-organellar contact sites. These innovations have led to discoveries regarding organelle interconnections, revealing mechanisms underlying metabolic processes such as cholesterol metabolism, glucose metabolism, and lysosomal repair. In addition to highlighting the advancements in TurboID applications, this review delineates the evolving trends in organelle research, underscoring the transformative potential of these techniques to significantly enhance organelle-specific proteomic investigations.

Keywords: Endoplasmic reticulum; Lysosome; Mitochondria; Proteomics

DOI: https://doi.org/10.4196/kjpp.2024.28.6.495