bims-lypmec 2023-02-19 papers

Mol Cell Proteomics. 2023 Feb 13. pii: S1535-9476(23)00018-X. [Epub ahead of print] 100509

Multi Cell Line Analysis of Lysosomal Proteomes Reveals Unique Features and Novel Lysosomal Proteins.

Fatema Akter, Sara Bonini, Srigayatri Ponnaiyan, Bianca Kögler-Mohrbacher, Florian Bleibaum, Markus Damme, Bernhard Y Renard, Dominic Winter.

Lysosomes, the main degradative organelles of mammalian cells, play a key role in the regulation of metabolism. It is becoming more and more apparent, that they are highly active, diverse, and involved in a large variety of processes. The essential role of lysosomes is exemplified by the detrimental consequences of their malfunction, which can result in lysosomal storage disorders, neurodegenerative diseases, and cancer. Using lysosome enrichment and mass spectrometry, we investigated the lysosomal proteomes of HEK293, HeLa, HuH-7, SH-SY5Y, MEF, and NIH3T3 cells. We provide evidence on a large scale for cell-type specific differences of lysosomes, showing that levels of distinct lysosomal proteins are highly variable within one cell type, while expression of others is highly conserved across several cell lines. Using differentially stable isotope labeled cells and bimodal distribution analysis, we furthermore identify a high confidence population of lysosomal proteins for each cell line. Multi cell line correlation of these data reveals potential novel lysosomal proteins, and we confirm lysosomal localization for six candidates. All data are available via ProteomeXchange with identifier PXD020600.

Keywords: Lysosomes; Mass spectrometry; Posterior probability analysis; Proteomics; Superparamagnetic iron oxide nanoparticles (SPIONs)

DOI: https://doi.org/10.1016/j.mcpro.2023.100509

Bio Protoc. 2023 Jan 20. 13(2): e4599

In vivo Assessment of Lysosomal Stress in the Drosophila Brain Using Confocal Fluorescence Microscopy.

Felipe Martelli.

Lysosomes play a central role in signaling, nutrient sensing, response to stress, and the degradation and recycling of cellular content. Defects in lysosomal digestive enzymes or structural components can impair lysosomal function with dire consequences to the cell, such as neurodegeneration. A number of methods exist to assess lysosomal stress in the model Drosophila, such as specific driver and reporter strains, transmission electron microscopy, and the investigation of gene expression. These methods, however, can be time consuming and, in some cases, costly. The procedure described here provides a quick, reliable, and low-cost approach to measure lysosomal stress in the Drosophila brain. Using fluorescence confocal microscopy and the LysoTracker staining, this protocol allows for the direct measurement of lysosome size and number. This method can be used to assess lysosomal stress under a number of different genetic and environmental scenarios in the Drosophila brain.

Keywords: Brain; Fluorescence microscopy; Fruit fly; Insecticide; LysoTracker; Lysosomal stress; Lysosome

DOI: https://doi.org/10.21769/BioProtoc.4599

Biophys J. 2023 Feb 10. pii: S0006-3495(22)02651-0. [Epub ahead of print]122(3S1): 308a

Structural basis for mTORC1-dependent regulation of the lysosomal and autophagic transcription factor EB.

Zhicheng Cui, James H Hurley.

DOI: https://doi.org/10.1016/j.bpj.2022.11.1735

Biophys J. 2023 Feb 10. pii: S0006-3495(22)01363-7. [Epub ahead of print]122(3S1): 43a-44a

Structure of the hops tethering complex, a lysosomal membrane fusion machinery.

Arne Moeller, Dmitry Shvarev, Jannis Schoppe.

DOI: https://doi.org/10.1016/j.bpj.2022.11.447