Lysosome
A lysosome is a membrane-bound organelle that is found in all animal cells,, and rarely in plant cells. There are normally hundreds of lysosomes in the cytosol, where they function as the cell's degradation center. Their primary responsibility is catabolic degradation of proteins, polysaccharides and lipids into their respective building-block molecules: amino acids, monosaccharides, and free fatty acids. The breakdown is done by various enzymes, for example proteases, glycosidases and lipases.
With an acidic lumen limited by a single-bilayer lipid membrane, the lysosome holds an environment isolated from the rest of the cell. The lower pH creates optimal conditions for the over 60 different hydrolases inside.
Lysosomes receive extracellular particles through endocytosis, and intracellular components through autophagy. They can also fuse with the plasma membrane and secrete their contents, a process called lysosomal exocytosis. After degradation lysosomal products are transported out of the lysosome through specific membrane proteins or via vesicular membrane trafficking to be recycled or to be utilized for energy.
Aside from cellular clearance and secretion, lysosomes mediate biological processes like plasma membrane repair, cell homeostasis, energy metabolism, cell signaling, and the immune response.
Discovery
, a Belgian scientist at the Laboratory of Physiological Chemistry at the Catholic University of Louvain, is credited with discovering lysosomes in the 1950s. De Duve and his team were studying the distribution of hydrolytic enzymes such as acid phosphatase within cells, using cell fractionation methods to isolate subcellular components. De Duve and his team identified an unknown organelle that was rich in acid phosphatase. This led them to propose the existence of lysosomes as membrane bound organelles containing digestive enzymes capable of breaking down a variety of biological molecules.Using differential centrifugation and enzyme activity assays, the team confirmed the hypothesis and understood that these organelles play a crucial role in intracellular digestion processes, such as phagocytosis and autophagy. The presence of digestive enzymes was further validated using electron microscopy. De Duve's discovery laid the foundation for new research into lysosomal functions and understanding disorders which could lead to undigested materials accumulating in the cell. De Duve was awarded the Nobel Prize in Physiology or Medicine in 1974.
Function and structure
Lysosomes vary in shape and size depending on their state, what they are digesting, and the cell type they are in. Their shape can differ from spherical and ovoid to occasionally tubular. The size of lysosomes ranges from 0.1-1.2 μm, with some tubular ones reaching up to 15 μm in phagocytes. Several hundred lysosomes can be found within a single cell. However, upon nutrient deprivation or induced autophagy, their numbers can drop below 50 in a cell.Lysosomes contain a variety of enzymes that enable the cell to break down various biomolecules it engulfs, including peptides, nucleic acids, carbohydrates, and lipids. The enzymes responsible for this hydrolysis require an acidic environment for optimal activity, with a pH ranging from ~4.5–5.0. The interior of the lysosome is acidic compared to the slightly basic cytosol.
The lysosomal membrane is a phospholipid bilayer with high carbohydrate content from heavily glycosylated membrane proteins. This forms a glycocalyx that protects the cell from the degradative enzymes held within the lysosome. Lysosomal hydrolases are pH-sensitive and do not function properly in the alkaline environment of the cytosol, ensuring that molecules and organelles in the cytosol are not degraded if there is leakage of hydrolytic enzymes from the lysosome.
In addition to breaking down polymers, lysosomes are capable of killing and digesting microbes, cells, or cellular debris. Through cooperation with phagosomes, lysosomes conduct autophagy, clearing out damaged structures and forming simple compounds, which are then used as new building materials. Similarly, lysosomes break down virus particles or bacteria during phagocytosis in macrophages.
Lysosomes also help detect pathogens through toll-like receptors, like TLR7 and TLR9. Microbes can be degraded into antigens, which are then loaded onto MHC molecules and presented to T-cells, a critical part of immune defense. Additionally, lysosomal enzymes can trigger lysosomal-mediated programmed cell death if released into the cytoplasm.
To maintain their acidic environment, lysosomes pump protons from the cytosol into the lysosomal lumen via a proton pump in the lysosomal membrane. Vacuolar-ATPases are responsible for the transport of protons, while the counter transport of chloride ions is performed by ClC-7 Cl⁻/H⁺ antiporter. This mechanism helps maintain a steady acidic environment, as well as ionic homeostasis, within the lysosome.
Lysosomes also help balance cellular metabolism by sensing nutrient availability. When nutrients are plentiful, they activate mTOR signaling to support anabolic processes. During starvation, lysosomes degrade autophagic material, recycling components to maintain cell survival.
Lysosomal degradation pathways
The lysosome is delivered material for degradation via transient interactions or complete fusion, forming endolysosomes and autolysosomes respectively. This way, the lysosomes act as reservoirs for acidic hydrolases, cycling through fusion and fission events with late endosomes and autophagosomes. The actual breakdown of endocytic and autophagic cargo primarily happens within these transient structures—endolysosomes and autolysosomes—under normal physiological conditions.Endocytosed materials – such as complex lipids, membrane proteins, and polysaccharides – enter the endocytic pathway; moving first in early endosomes, then in late endosomes containing intraluminal vesicles. Then they interact with lysosomes, either via full fusion, or via "kiss-and-run" events where brief membrane contact allows content exchange before the organelles separate. The resulting hybrid structure is called an endolysosome.
Intracellular materials – like damaged organelles or misfolded proteins – are processed through the autophagic pathway. Autophagy, or "self-eating," is a continuous cellular process that delivers cytosolic components to lysosomes for degradation. There are three main types of autophagy: macroautophagy, microautophagy, and chaperone-mediated autophagy —each differing in how cargo is delivered to the lysosome. After merging with lysosomes they create hybrid organelles called autolysosomes.
- Macroautophagy involves the formation of isolated double- or multi-membranes that encapsulate portions of cytosolic material such as misfolded- or polyubiquitinated proteins, lipids, damaged or aged organelles, RNA, and fragments of the ER. These vesicles mature into autophagosomes and then fuse with lysosomes for degradation, creating an autolysosome. A key marker of autophagosomes is LC3-II, a lipidated form of microtubule-associated protein light chain 3 that appears early in the process and is broken down during digestion
- Microautophagy bypasses vesicle formation altogether, with lysosomes directly engulfing surrounding cytosolic material through membrane invagination; pinocytosis. This process is similar to the formation of intraluminal vesicles in MVBs.
- Chaperone-mediated autophagy selectively degrades proteins that contain a KFERQ motif. These substrates are recognized by Hsc70, which binds them and delivers them to lysosomes via the receptor LAMP-2A for degradation.
Because catabolic and anabolic pathways are interconnected and tightly regulated, the flow of cargo through the endocytic and autophagic systems is modulated by cellular signaling and nutrient availability. Nutrient deprivation, for example, activates autophagy, which is then halted once lysosomal degradation is complete. Lysosomes themselves play a direct role in sensing nutrient levels through the lysosomal nutrient-sensing system, which includes components such as V-ATPase, Rag GTPases, and the mTOR complex.
Formation
The formation of lysosomes begins in the endoplasmic reticulum, where hydrolytic enzymes are synthesized. These enzymes are then transported to the Golgi apparatus, where they undergo modifications to ensure proper targeting and function. The enzymes are tagged with mannose-6-phosphate, allowing them to be sorted into vesicles. These vesicles then bud off from the trans-Golgi network and fuse with early endosomes.Early endosomes degrade cargo from the extracellular environment, and as they mature into late endosomes, proton pumps are activated, causing the internal environment to become acidic. This acidic environment activates the hydrolytic enzymes, which further mature the endosome into a lysosome. The lysosome then breaks down and recycles cellular waste.
Disruptions in lysosomal formation can lead to dysfunctional lysosomes and the accumulation of undigested molecules, contributing to various lysosomal storage disorders.
Pathogen entry
Lysosomes are a crucial component of the innate immune system and play an important role in defending the cell against pathogens such as viruses or bacteria. When a pathogen enters the cell, it is often enclosed in a phagosome, which then fuses with a lysosome to form a phagolysosome where the hydrolytic enzymes break down the pathogen.Lysosomes also play a big role in the adaptive immune system. Fragments of pathogens that have been broken down by phagolysosomes are sent to the major histocompatibility complex class II and presented on the surface of antigen presenting cells. This then activates helper T cells, which causes an adaptive immune response.
Just like other pathogens, viruses entering the cell via endocytosis are degraded in lysosomes. However, some viruses have evolved strategies to escape degradation by lysosomes, and are able to escape the lysosome before complete degradation and spread viral material into the cytoplasm which then spreads viral infection in the cell. Poor lysosomal activity and failure by lysosomes to properly degrade all biomolecules from pathogens results in higher viral infections by viruses such as HIV.