Lysosomes are one of the major compartments responsible for degradation of biological macromolecules within the cell. The majority of these originate from endocytosis, phagocytosis or autophagocytosis, but some proteins that are targeted for degradation can also be directly translocated into lysosomes. Lysosomes are highly acidic and contain a plethora of hydrolytic enzymes, which are isolated from the cytosol by a single phospholipid bilayer. The membrane contains many molecules that facilitates and carefully regulates their fusion with late endosomes, phagosomes and autophagosomes, as well as transport proteins that mediate the export of monomeric metabolites that result from the degradation of macromolecules in lysosomes, thereby enabling them to be recycled. Recent discoveries have revealed that lysosomes interact with many other cellular structures, and play roles in a variety of cellular processes, including metabolic signalling, cell adhesion and migration, plasma membrane repair, and gene regulation.
Lysosomes are highly dynamic, varying in numbers and size in response to environmental and cellular cues. Similar to endosomes, lysosomes are often located close to the Golgi apparatus, but tend to be larger. However, differentiation between different types of vesicles in the endomembrane system requires co-staining with marker dyes or of marker proteins. Therefore, vesicle-like stainings are annotated as "vesicles" in the Cell Atlas, while the terms "endosomes", "lysosomes" and "peroxisomes" are only used if colocalization experiments have been carried out.
Read more about the proteome of lysosomes as a substructure of vesicles.