Endosome Maturation and SNARE Proteins

Intracellular Organization and Trafficking

• Eukaryotic cells have the same basic set of membrane-enclosed organelles
• Organelles have different internal environments compared to the surrounding cytosol due to membranes
• Major intracellular compartments in an animal cell include: mitochondrion, Golgi apparatus, smooth endoplasmic reticulum, nucleolus, rough endoplasmic reticulum, endosome, lysosome, cytosol, peroxisome, and free ribosomes
• Proteins travel between organelles in various ways: protein translocation, gated transport, vesicular transport, and engulfment
• Sorting signals within the amino acid sequence of a protein direct its movement. These signals are recognized by sorting receptors present in different organelles
• The secretory pathway’s environment is similar to the outside of a cell
• The synthesis of phospholipids takes place in the ER membrane. The lipids are only formed in one of the two layers of the bilayer that faces the cytosol. The ER assembles most lipid bilayers

Biomolecule Condensates

• Cells also have biomolecule condensates, places with high concentrations of certain nucleic acids and proteins serving as biochemical factories
• Specific biomolecule condensates include: nucleolus, pyrenoid, stress granules, P-granules, Balbiani body, Cajal body, paraspeckles, RNA transport granule, PML body, and postsynaptic density
• Biomolecule condensates can include a series of macromolecules (nucleic acids and/or proteins) that serve as a scaffold for the whole condensate
• These scaffolds attract and recruit other proteins and/or nucleic acids, which perform specific tasks
• The nucleolus is an example of a biomolecule condensate that is involved in rRNA transcription, ribosome assembly, and pre-rRNA processing
• The nucleolus is composed of dense and granular components.

The Endoplasmic Reticulum

• The ER plays a significant role in the biosynthesis of lipids and proteins
• It stores Ca²⁺ ions, which are used in various cellular processes
• The ER is an interconnected network of tubules and flattened sacs, continuous with the outer nuclear membrane
• The ER extends throughout the entire cytosol, with all regions close to some portion of the ER membrane
• The ER is structurally and functionally diverse, with rough ER (with ribosomes) for the secretory pathway and smooth ER (without ribosomes) for lipid biosynthesis and metabolism
• The proportion of rough ER to smooth ER varies among cell types

Proteins Present in the ER

• Proteins that need to be secreted, resident proteins of the ER and Golgi, and transmembrane proteins are produced in the ER

• The process of protein translocation across the ER membrane may or may not require ongoing polypeptide chain elongation.

  • Co-translational translocation
  • Post-translational translocation

• Proteins that need to be embedded in the cell membrane commonly contain hydrophobic segments which are recognized like signal sequences

• Some proteins are integrated into the ER membrane by a post-translational mechanism using chaperones like Get3

• Some membrane proteins acquire a covalently attached glycosylphosphatidylinositol (GPI) anchor.

• After the completion of protein synthesis, the precursor protein remains anchored to the ER membrane by a hydrophobic C-terminal sequence, while the rest of the protein is in the ER lumen. This process is managed through the action of a transamidase enzyme.

• Resident ER proteins include translocons and receptors, signal peptidase, chaperones that aid proper folding, proteins that catalyze disulfide bonds, proteins that add polysaccharides to proteins (glycosylation), and proteases

• Specialized proteins that fold other proteins in the ER

The Endocytic Pathway

• Cells take up molecules from the outside via endocytosis, a process through which endocytic vesicles containing the materials from the outside fuse into the cell.
• Recycling endosomes serve as intracellular protein storage sites. The protein storage is mobilized as needed
• Endocytic vesicles form primarily from clathrin-coated regions of the plasma membrane, though there are exceptions
• Early endosomes mature into late endosomes
• ESCRT protein complexes mediate the formation of intralumenal vesicles in multivesicular bodies, where intralumenal vesicles (small membrane-bound vesicles inside a bigger compartment) are used to transport materials among different parts of the cell.

The Golgi Apparatus

• The Golgi apparatus is an ordered series of flattened, membrane-enclosed compartments (cisternae) connected by tubular connections.
• Materials pass between the cisternae in either vesicular transport or cisternal maturation mechanisms
• The Golgi apparatus also processes proteins, including modifying/ removing/ substituting original sugars added at the ER and adding extra sugars elsewhere. This is carried out by Golgi resident proteins at different parts of the Golgi, a complex process that has been coined as glycosylation
• The final step in the Golgi process is sorting of each vesicle into the correct compartment.

Autophagy

• Autophagy is a cellular process where a portion of the cell's cytoplasm (including organelles and proteins) is engulfed in a double-membrane structure called the autophagosome, and then sent to lysosomes to degrade the contents
• Autophagy can occur for these reasons: During starvation to supply with materials to survive, damaged organelles are repaired or replaced, specific structures are removed during development or in changing conditions, presence of bacteria or viruses inside cells, and presence of macroaggregates.
• Many more reasons also trigger autophagy, as well

Lysosomes

• Lysosomes are the terminal destination for degradation of proteins, microorganisms, dead cells, and other ingested materials.
• The lysosome lumen contains a low pH that is maintained by a H⁺ pump.

Mechanisms of Membrane Transport and Compartment Identity

• Vesicles and compartments have different types of coat proteins, phosphoinositides (e.g., PIPs), Rab proteins, v-SNARES and t-SNARES, therefore, establishing identity. Different coat-proteins and their properties facilitate many different kinds of transport pathways, including the ER to Golgi and vesicle to compartment.
• The assembly and disassembly of clathrin-coated vesicles involve the interaction between adaptor proteins and various membrane-bending and fission proteins. The assembly of the coat introduces curvature into the membrane
• Dynamin is in charge of pinching off clathrin-coated vesicles
• Polymerization of actin filaments occurs near the vesicle neck, and helps transport the budding vesicle away from the plasma membrane

Cholesterol Transport

• LDL contains a core of cholesterol esters
• LDL is recognized by LDL receptors in the plasma membrane to form a clathrin-coated vesicle
• The vesicle fuses to other vesicles, forming the early endosome; the clathrin coat is lost.
• As the acidity increases, the LDL particle dissociates from the LDL receptor, and the LDL is retained in the lumen
• The endosome matures into a endolysosome and lysosomes to be used by the cell for membrane production.

This quiz explores the intricate process of endosome maturation, focusing on the transition from early to late endosomes. It covers pH changes, the role of SNARE proteins in membrane fusion, and the connection to the trans-Golgi network. Test your knowledge on the specifics of cholesterol transport and the characteristics of late endosomes.