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Questions and Answers
What is the role of Multivesicular Bodies (MVBs) in cargo trafficking?
What is the role of Multivesicular Bodies (MVBs) in cargo trafficking?
Which pathway does cargo follow when it is not recycled?
Which pathway does cargo follow when it is not recycled?
What triggers the activation of receptors at the plasma membrane?
What triggers the activation of receptors at the plasma membrane?
What characteristic of Multivesicular Bodies (MVBs) aids in their function?
What characteristic of Multivesicular Bodies (MVBs) aids in their function?
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What effect does receptor activation have after ligand binding?
What effect does receptor activation have after ligand binding?
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What role does VPS4 play in the ESCRT complex?
What role does VPS4 play in the ESCRT complex?
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How does viral shedding utilize the ESCRT machinery?
How does viral shedding utilize the ESCRT machinery?
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What is a primary function of autophagy?
What is a primary function of autophagy?
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What structural feature is essential for the formation of an autophagosome?
What structural feature is essential for the formation of an autophagosome?
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Which of the following best describes the relationship between endocytosis and autophagy?
Which of the following best describes the relationship between endocytosis and autophagy?
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What is the primary role of dynein motors in cellular transport?
What is the primary role of dynein motors in cellular transport?
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What structural feature do golgins possess that aids in vesicle tethering?
What structural feature do golgins possess that aids in vesicle tethering?
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What happens to lysosomes when dynein function is disrupted?
What happens to lysosomes when dynein function is disrupted?
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Which of the following components binds to the N-terminal stem of dynein?
Which of the following components binds to the N-terminal stem of dynein?
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What triggers the power stroke in dynein-mediated movement?
What triggers the power stroke in dynein-mediated movement?
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What type of complex is necessary for dynein-mediated vesicle transport?
What type of complex is necessary for dynein-mediated vesicle transport?
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What characteristic of dynein allows it to transport different types of cargo?
What characteristic of dynein allows it to transport different types of cargo?
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Which region of dynein is responsible for interacting with microtubules?
Which region of dynein is responsible for interacting with microtubules?
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What is the primary function of vesicle coat proteins?
What is the primary function of vesicle coat proteins?
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Which type of vesicle is responsible for transporting materials from the Golgi complex back to the ER?
Which type of vesicle is responsible for transporting materials from the Golgi complex back to the ER?
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How do clathrin coated vesicles primarily form?
How do clathrin coated vesicles primarily form?
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What triggers the release of the viral membrane glycoprotein VSV-G from the ER?
What triggers the release of the viral membrane glycoprotein VSV-G from the ER?
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What role does endocytosis play in cellular function?
What role does endocytosis play in cellular function?
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What defines the specific pathways of vesicle trafficking indicated by color coding?
What defines the specific pathways of vesicle trafficking indicated by color coding?
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Which of the following describes the requirement for vesicle transport?
Which of the following describes the requirement for vesicle transport?
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What is the significance of the Golgi complex in protein transport?
What is the significance of the Golgi complex in protein transport?
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Which type of coated vesicle is involved in endocytosis?
Which type of coated vesicle is involved in endocytosis?
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What is the function of Atg8 in the autophagosome process?
What is the function of Atg8 in the autophagosome process?
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In what situation does autophagy become a non-selective process?
In what situation does autophagy become a non-selective process?
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What role do polyubiquitin chains play in the autophagy process?
What role do polyubiquitin chains play in the autophagy process?
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What is formed when the autophagosome fuses with the lysosome?
What is formed when the autophagosome fuses with the lysosome?
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Which of the following components is NOT involved in autophagosome maturation and lysosomal fusion?
Which of the following components is NOT involved in autophagosome maturation and lysosomal fusion?
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During the fusion events of the autophagosome, what change occurs internally?
During the fusion events of the autophagosome, what change occurs internally?
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What is the main purpose of selective autophagy?
What is the main purpose of selective autophagy?
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Which process is activated when there are low levels of ATP or amino acids?
Which process is activated when there are low levels of ATP or amino acids?
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What role does Atg8/LC3 play in selective autophagy?
What role does Atg8/LC3 play in selective autophagy?
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What is a primary function of WASP in actin polymerization?
What is a primary function of WASP in actin polymerization?
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What is the direction of transport for dynein motor proteins?
What is the direction of transport for dynein motor proteins?
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Which component is primarily responsible for vesicle transport along actin filaments?
Which component is primarily responsible for vesicle transport along actin filaments?
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How does the Arp2/3 complex contribute to cell motility?
How does the Arp2/3 complex contribute to cell motility?
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What happens to G-actin when it gets loaded onto an F-actin filament?
What happens to G-actin when it gets loaded onto an F-actin filament?
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Which structure acts as a sorting station for cargo between the ER and Golgi?
Which structure acts as a sorting station for cargo between the ER and Golgi?
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What is the function of myosin V in organelle transport?
What is the function of myosin V in organelle transport?
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Which factor activates Arp2/3 during Listeria motility?
Which factor activates Arp2/3 during Listeria motility?
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What type of interaction keeps WASP in an inactive state within the cytosol?
What type of interaction keeps WASP in an inactive state within the cytosol?
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What occurs during actin treadmilling at physiological concentrations?
What occurs during actin treadmilling at physiological concentrations?
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Which component of the cytoskeleton is primarily involved in long-range transport of vesicles?
Which component of the cytoskeleton is primarily involved in long-range transport of vesicles?
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What is the angle of branching between old and new filaments formed by Arp2/3?
What is the angle of branching between old and new filaments formed by Arp2/3?
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What plays a significant role in the recycling of actin during vesicle transport?
What plays a significant role in the recycling of actin during vesicle transport?
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Study Notes
Vesicle Transport and Cargo Delivery
- Vesicles bud off and fuse with different compartments
- Carry 'cargo' — membrane-associated and soluble molecules
- Each vesicle must be selective for certain cargo and fuse with the appropriate target membrane
- The endomembrane system divides the cell into different membrane-bound compartments
- It regulates the translation, modification, and trafficking of proteins
- It turns on/off signal transduction
- It includes:
- nuclear envelope
- endoplasmic reticulum
- Golgi apparatus
- secretory vesicles
- endosomes
- lysosomes
- autophagosomes
- plasma membrane
Reading List
- Chapters 14–Introduction, 14.2, 14.3 (first half), 14.4 (limited), 14.5, 14.6; Chapter 17 – intro, 17.1, 17.2, 17.3, 17.5; Chapter 18 – intro, 18.1, 18.2, 18.4
- Chapters 13 and 16
- Two review articles on vesicle coat proteins and Rab GTPases on Blackboard
Learning Outcomes
- Explain the requirements for vesicle transport
- Describe the different types of vesicle coat proteins and their functions
- Describe the molecular composition of clathrin-coated vesicles
- Explain the mechanism of clathrin coat formation
- Describe dynamin function
Vesicle Coat Proteins
- The transport vesicles usually have coat proteins that:
- Provide shape to membranes to "curve" and bud
- Determine the size and shape of the vesicle
- Concentrate the protein in the vesicle
- Provide selectivity for the "cargo"
- Determine the vesicle's destination
- Clathrin
- COPI
- COPII
Vesicle Transport and Coated Vesicles
- Clathrin-coated vesicles — trans-Golgi network (TGN) to endosome and plasma membrane (via endocytosis)
- COPI coated vesicles — Golgi complex to the ER (retrieval)
- COPII coated vesicles — ER to Golgi
Different Ways Proteins Associate with Lipid Membrane
- Anchored within cytosolic face by amphipathic α-helix
- Covalent attachment of lipid group — fatty acid or prenyl group
- Non-covalent interactions with other membrane-bound proteins — peripheral membrane protein
Clathrin-Coated Vesicles
- Transport material from plasma membrane and between endosomes and Golgi apparatus
- Clathrin subunits are made up of 3 large (heavy chain) and 3 small polypeptides (light chain) that assemble in "triskelions" at the trans-Golgi network (TGN) or at plasma membrane
- Clathrin forms an outer protein lattice
Endocytosis
- Engulfment of extracellular molecules occurring at the plasma membrane
- Regulates receptor signaling, receptor turnover, nutrient uptake, polarity, cell migration, neurotransmission
- Receptor-mediated endocytosis
- Clathrin-dependent
- Caveolin-dependent (lipid rafts, sphingolipids, GPI anchored proteins)
- Clathrin- and Caveolin-independent
- Phagocytosis
- Pinocytosis
Clathrin Coat Formation
- During endocytosis at plasma membrane — recruitment of AP2 adaptor protein complex is required for clathrin recruitment, coat assembly (formation of clathrin-coated pits), and eventual budding
- AP2 adaptor protein binding to specific phospholipids results in conformational change that allows binding to cargo receptors on cell surface, triggers membrane curvature
AP Adaptor Protein Complex
- AP-2 adaptor protein complex is heterotetrameric, multi-subunit
- α-adaptin
- β2-adaptin
- σ2-chain
- μ2-chain
- AP-2 on clathrin-coated vesicles originating from the plasma membrane (endocytosis)
- AP-1 adaptor complex (Golgi)
- Recognizes specific peptide motifs on the cargo receptor (endocytosis signals)
- Interacts with plasma membrane lipids, cargo, and clathrin
Assembly of a Clathrin Coat
- Protein "cargo" binds to a membrane-bound receptor protein (e.g., mannose-6-P receptor on Golgi)
- The receptors only selectively recruit the correct cargo for the vesicle
- The receptor also binds adaptor proteins (e.g., AP-1 complex), which in turn binds to the triskelion clathrin
Assembly of a Clathrin Coat
- Many "cargo-receptor-adaptin-clathrin" complexes form in a clathrin-coated vesicle
- Vesicle formation and budding is assisted by dynamin (requires GTP)
- The clathrin coat dissociates immediately & components are recycled — leaving behind an uncoated vesicle that is transported to its destination
Membrane Fission by Dynamin
- Dynamin oligomerises and forms a helical ring around the neck of the bud, recruits other proteins, and tethers itself to the membrane through lipid-binding domains
- Dynamin constricts in the presence of GTP
- GTP hydrolysis of dynamin results in the lengthwise extension of helix, and fission of membrane
Understanding Dynamin Function
- Use of temperature-sensitive mutants to understand dynamin function in vesicle scission
- Ts mutations in dynamin (e.g., Drosophila "Shibire") halt vesicle fission and allow visualization of arrested buds
- Results in immediate paralysis of the flies — but is reversible upon return to permissive temperature
Clathrin-Coated Vesicles and Transport to Lysosomes
- Acid hydrolase enzymes are N-glycosylated, then phosphorylated on mannose-6 in Golgi, allowing binding to M6P-receptor and trafficking to lysosome
Questions to Consider
- What are the requirements for vesicle transport?
- What is the role of the clathrin coat?
- How is the clathrin-coat assembled?
- Explain the mechanisms of AP-2 adaptor regulation and function during clathrin-mediated vesicle formation.
- How does dynamin regulate vesicle fission?
Learning Outcomes
- Explain the mechanism of COP I and II coated vesicle formation
- Describe the role of Rab GTPases in vesicle transport
- Explain how Rabs are regulated during vesicle transport
- Describe how Rabs contribute to vesicle fusion
- Explain the mechanisms of SNARE-mediated vesicle fusion
Vesicle Transport and Coated Vesicles
- Clathrin-coated vesicles — trans-Golgi network (TGN) to endosome and plasma membrane (via endocytosis)
- COPI coated vesicles — Golgi complex to the ER (retrieval)
- COPII coated vesicles — ER to Golgi
Formation of COP II Vesicles
- The COP II coat has 5 protein subunits and also has an associated GTPase (Sar1)
- COP II interactions carry bulk protein but also specifically recruit:
- enzymes for Golgi processing (e.g., glycosyltransferases)
- docking and fusion proteins
- integral proteins that bind to specific “cargo”
Formation of COP II Vesicles
- Sar1-GEF (Sec12) is embedded in donor membrane
- Recruits and activates Sar1 loading with GTP
- Sar1-GTP recruits Sec23/24 which interacts with cargo, forming inner coat
- Sec13/31 forms the outer coat
COP I Vesicles and Retrograde Transport
- COP I coated vesicles retrieve proteins from Golgi back to the ER
- ER proteins have KDEL (Lys-Asp-Glu-Leu) at C-terminus, recognized by a KDEL receptor in cis-Golgi, and retrieved by interaction with COP I
- COP I coat:
- α-COP, β'-COP, E-COP, B-COP,
- σ-COP, γ-COP and ζ-COP
- ARF1 GTPase is required for coatomer recruitment, recruited and activated by Golgi-localised GEF proteins
- These GEFs replace GDP with GTP to activate ARF1
Key protein complexes and GTPases associated with each type of coated vesicle
- See the table in the document for details.
Importance of GTPases
- Each type of coated vesicle has an associated GTPase (e.g., Sar1 in COPII vesicles, ARF in COPI and clathrin-coated vesicles)
- GTP-loaded ARF or Sar1 binds to effector proteins, facilitating coat assembly
- GTP hydrolysis is required for coat disassembly
- Dynamin is a GTPase involved in vesicle transport (Rab family)
Ras Family of Small GTPases
- Small guanosine triphosphatases (GTPases) — over 150 human members, divided into 5 major branches based on sequence (Ras, Rho, Rab, Ran, Arf)
- Binary molecular switches that share common biochemical mechanism and function as monomeric G proteins — GDP/GTP
- Post-translational modifications control subcellular localization and interactions with proteins that act as regulators and effectors
Rab GTPase Family
- Largest branch of Ras family (~ 61 members)
- Regulates intracellular transport of vesicles and proteins between organelles of the endocytic and biosynthetic pathway.
- Through interactions with effector proteins, facilitates vesicle formation, budding, transport, and vesicle fusion at acceptor site
- Subcellular localization and specificity for different intracellular compartments of each Rab is dependent on post-translational lipid modifications (prenylation) and effector interactions
Questions to consider
- What is endocytosis?
- How do receptors from the plasma membrane get turned off and transported to the lysosome?
- Describe the mechanism of intraluminal vesicle formation by ESCRTs.
- What is autophagy and how does it regulate cell homeostasis?
- What are the primary components of autophagy?
Autophagy
- Autophagy is a cytosolic degradation pathway
- Requires autophagosome — double membrane organelle
- Can degrade misfolded proteins, damaged organelles, or invading pathogens that escape out of phagosome into cytosol
- Also, can capture bulk cytosol to harvest energy and amino acids during times of starvation
- Autophagy has selective pathways that can select cargo to be captured by autophagosome or can non-selectively capture cytosol
- Atg8/LC3 plays a role in decorating the inner and outer leaflets of autophagosomes
- Autophagosome maturation leads to reduction in internal pH and acquisition of machinery to facilitate fusion with lysosome.
- This process leads to the formation of autolysosome resulting in proteolytic degradation of components during starvation or in cellular damage.
Endocytosis
- Endocytosis is the internalisation of extracellular molecules and plasma membrane receptors, which can be transported to the lysosome for their degradation
ESCRT Complexes
- ESCRT (endosomal sorting complexes required for transport) complex is required for intraluminal vesicle formation
- ESCRT-0 contains ubiquitin binding domain which interacts with ubiquitylated receptor cargo
- ESCRT-0 also contains binding domain for interaction with PI3P-rich phospholipid on endosomal membrane
- Multiple subsequent ESCRT proteins help shape the membrane to form an invagination and eventual budded intraluminal vesicle
- Hrs is an ESCRT-0 protein that interacts with ubiquitin on cargo
- VPS4 is an ATPase that hydrolyses ATP to disassemble ESCRT complex allowing intraluminal vesicle formation
Viral Shedding
- Virions bud off from plasma membrane surface using the ESCRT machinery
- Requires similar membrane bending to intraluminal vesicle formation
How do Transport Vesicles Identify Their Target Membrane?
- SNARE proteins are used (around 35 in mammals)
- Exist in pairs:
- v-SNARES on surface of vesicles
- t-SNARES on membrane of target
- v- and t-SNAREs have helices that interact with one another and dock the vesicle to the target membrane
- The interaction is initiated by a vesicle-specific Rab GTPase
Vesicle Docking
- Rab-GTP protein on vesicle surface binds to specific Rab effector in target membrane
- This brings v-SNAREs and t-SNAREs into close proximity allowing docking
- α-helices of v-SNARE and t-SNARE form coiled-coils (trans-SNARE complex)
- Exerts inward force that brings the two membranes close together
Membrane Fusion
- Mechanism of membrane fusion is unknown, but may be opposite to dynamin model
- Lipid bilayers fuse by flowing into each other after being forced into close proximity
- A complex of two proteins (NSF and α-SNAP) binds to the "empty" SNARE complexes (cis-SNARE complexes)
- ATP hydrolysis (catalysed by NSF) causes disassembly of the SNARE complexes and recycling
How do synaptic vesicles simultaneously and precisely release neurotransmitter?
- Delivery of synaptic vesicle membrane components to presynaptic plasma membrane
- Endocytosis of synaptic vesicle membrane components to form new synaptic vesicles directly → Endosomes
- Endocytosis of synaptic vesicle membrane components and delivery to endosome
- Budding of synaptic vesicle from endosome; loading of neurotransmitter into synaptic vesicle
- Secretion of neurotransmitter by exocytosis in response to an action potential
Mechanism of Coordinated Synaptic Membrane Fusion
- Synaptic vesicles dock at the presynaptic plasma membrane, with complexin keeping the trans-SNARE complex in a primed position
- Calcium induces a conformational change in the complex allowing coordinated vesicle fusion with plasma membrane leading to neurotransmitter release
Actin Cytoskeleton Review
- Are polarized, with (+) and (-) end
- Composed of G-actin subunits that assemble into F-actin filaments
- ATP-G-actin gets loaded on filament and undergoes hydrolysis before release from filament
- Undergo actin treadmilling
- At physiological concentrations — G-actin gets preferentially added to (+) end, while being preferentially disassembled from (-) end
Actin and Vesicle Transport
- Proteins associated with endocytic vesicles and the clathrin coat also recruit actin nucleation-promoting factors
- WASP is one of these nucleation-promoting factors that activates Arp2/3 complex
- Arp2/3 promotes actin polymerization, which drives internalized vesicles away from the plasma membrane
WASP and Arp2/3 Activation
- Wiscott Aldrich Syndrome protein (WASP) is an actin nucleation-promoting factor
- WASP is held inactive in cytosol through intramolecular interaction that masks WCA domain
- Following interaction with active GTPase (Cdc42-GTP) through RBD motif, intramolecular interaction is relieved and W domain is exposed to bind actin and the A domain activates Arp2/3
Arp2/3 Complex and Actin Branching
- WASP binding to Arp2/3 results in conformational change in complex and allows Arp2/3 binding to pre-existing actin filaments
- Actin subunit gets brought in by W domain of WASP and together binds to Arp2/3 to initiate actin nucleation
- Nucleation at (+) end occurs and filament extends
- Angle between old and new filament is 70°
Listeria Use of Similar Methods for Motility
- Listeria monocytogenes is a food-borne pathogenic bacteria that causes gastroenteritis
- Enters the cell, divides, and hijacks the cell motility machinery for its own gain
- Moves from one cell to the other, it moves inside the cell by polymerizing actin into a comet tail and pushing its way through the plasma membrane to get to the adjacent cell
Relationship to Arp 2/3 Function During Cell Motility
- Arp 2/3 activation and formation of branched actin at leading edge promotes membrane protrusion, which is required for a cell to migrate in the forward direction
The Cytoskeleton and Vesicle Transport
- Newly formed vesicles associate with the actin cytoskeleton through adaptor proteins
- Actin motor proteins called myosins either tether vesicles to actin cytoskeleton or transport vesicles along the actin cytoskeleton — facilitates cargo delivery and fusion events
Actin-Binding Myosin Motor Proteins
- Each myosin is composed of an actin-binding head domain and lever arm neck domain
- May also contain a cargo-binding tail domain that interacts with membrane lipids or adaptor proteins
- All motor head domains convert ATP hydrolysis into mechanical movement
- Function as monomer or dimer to tether or transport cargo along actin filaments
- Common classes of myosins: I ,II, and V
Myosin V Function in Organelle Transport
- Functions as a dimeric motor protein
- Moves towards (+) end of actin filament
- Has a step size of 30-40 nm, which is ATP dependent
- In budding yeast, myoV is essential to transport mitochondria to newly formed bud
The Microtubule Network
- 2 types of microtubule motor proteins:
- Dynein — move towards (-) end
- Kinesins — move towards (+) end
- Transport vesicles or organelles
- Involved in long-range and fast transport (compared to short-range and slower transport of myosins)
ER and Golgi Transport
- ER, where membrane and soluble, secreted cargo is translated and trafficked toward Golgi
- Intermediate compartment between ER and Golgi, called vesicular tubular cluster or ER-Golgi intermediate compartment (ERGIC)
- COPII vesicles lose their coats and fuse to form the vesicular tubular cluster
- This organelle serves as a sorting station for cargo between ER and Golgi
Microtubules Maintain ER and Golgi Structure
- Microtubule motor proteins are essential to maintain the structure and organization of the ERGIC and the Golgi
- Dynein-dependent and kinesin-dependent transport of vesicles
- Dynein motors are essential for Golgi positioning — aligns in the perinuclear region and along the axis of cell polarity
Microtubules and Golgi Vesicle Formation
- Golgins are large proteins (over 30 genes), with coiled-coil domains adopting a rod-like shape
- Golgins involved in transport and vesicle tethering around regions of the Golgi
- Act as Rab effector proteins
- Golgins interact directly with microtubules, with microtubule-associated proteins or microtubule motors, such as dynein
- Contribute to Golgi positioning and morphology
Microtubule-Mediated Transport Along Endocytic Route
- Kinesin- and dynein-dependent transport essential along endocytic route to transport vesicular cargo between various compartments
- Lysosomes are positioned in perinuclear regions — loss of dynein leads to a dispersal of lysosomes throughout the cytoplasm
Dynein Structure
- One gene encoding cytoplasmic dynein heavy chain
- Cytoplasmic dynein complex contains a pair of identical heavy chains (homodimer)
- Dynein heavy chain has an ATP-dependent motor (head), microtubule binding stalk region, and N-terminal stem that binds cargo
Dynein-Mediated Movement
- Each motor head domain contains a hexameric AAA ring — that has stalk, buttress, and linker regions protruding from AAA ring
- Conformational change of head relative to stem, leading to movement of stalk domain, triggers the power stroke that results in movement
Dynein-Mediated Movement
- Stalk region interacts with microtubules, ATP-dependent motor domain performs the work
- Dynein in the presence of ATP has low affinity for microtubules, ATP hydrolysis by AAA domains in motor head leads to microtubule binding, release of Pi results in conformational change (power stroke) and 8 nm step size of dynein
Dynein-dynactin Complex and Vesicle Transport
- How does 1 dynein gene regulate the transport of many, distinct cargo?
- Dynein cannot function by itself, transport requires dynactin — a large complex linking dynein to cargo and regulating dynein activity
- This complex can interact with a range of adaptor proteins, thereby providing specificity for different cargo.
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Description
Explore the complex roles of Multivesicular Bodies (MVBs) in cargo trafficking and their interaction with other cellular mechanisms, such as autophagy and the ESCRT complex. This quiz delves into essential pathways, receptor activation, and the structural features that underpin these processes.