L12 - RNA virus replication structure Flashcards
1
Q
What is a model RNA virus used to study replication structures?
A
Flock House Virus (FHV), which infects insects.
2
Q
Why do viruses induce structural changes in host cells?
A
To create specialized compartments that enhance replication efficiency.
3
Q
What cellular components are involved in virus-induced structures?
A
Cell membranes, the cytoskeleton, and inter-organelle contacts.
4
Q
What are virus replication factories?
A
Intracellular compartments where viruses replicate and assemble new particles.
5
Q
What is the role of host factors in virus replication factories?
A
They provide scaffolding and metabolic support for viral replication.
6
Q
How do viruses manipulate host cells to form replication factories?
A
By altering metabolic and signaling pathways.
7
Q
Why do viruses use membrane-bound replication compartments?
A
To increase replication efficiency by concentrating substrates and enzymes.
8
Q
How do these compartments protect viruses from host defenses?
A
They shield viral replication intermediates like dsRNA from immune detection.
9
Q
What process is spatially coordinated in these compartments?
A
Viral replication, translation, and assembly.
10
Q
What imaging technique is used to study virus replication factories?
A
Transmission electron microscopy (TEM).
11
Q
How does TEM help visualize virus structures?
A
It provides high-resolution images of virus-induced cellular changes.
12
Q
What is a limitation of TEM?
A
It provides static images and requires complex sample preparation.
13
Q
What high-resolution imaging technique is used for SARS-CoV-2 replication structures?
A
Cryo-electron tomography (Cryo-ET).
14
Q
Why is Cryo-ET useful for studying virus lifecycles?
A
It allows visualization of viral replication complexes in near-native conditions.
15
Q
What cellular structures are altered by SARS-CoV-2 replication?
A
Endoplasmic reticulum (ER)-derived double-membrane vesicles.
16
Q
How many proteins does Flock House Virus (FHV) encode?
A
Four proteins.
17
Q
What is the advantage of using FHV as a model?
A
Its simplicity allows detailed study of RNA virus replication mechanisms.
18
Q
Where does FHV replication occur within the cell?
A
On the outer membrane of mitochondria.
19
Q
What method is used to identify host factors involved in viral replication?
A
siRNA screening
20
Q
How does siRNA screening help in virus research?
A
It allows systematic identification of host proteins essential for viral replication.
21
Q
What was discovered about West Nile Virus using siRNA screening?
A
siRNA screening identified host factors essential for West Nile Virus replication, including proteins involved in RNA binding, membrane remodeling, and intracellular trafficking.
22
Q
What role do RNA-binding proteins play in viral replication?
A
They assist in RNA recruitment and strand synthesis.
23
Q
Why are cellular chaperones important for viruses?
A
They help in protein folding and complex assembly.
24
Q
How do viruses manipulate membrane lipids for replication?
A
They enrich specific lipids like phosphatidylinositol-4-phosphate (PtdIns4P) to modify membranes.
25
What is a DMV in viral replication?
A double-membrane vesicle that houses viral RNA synthesis.
26
How do convoluted membranes (CMs) contribute to virus replication?
They serve as sites for viral protein synthesis and processing.
27
What is a reticulovesicular network (RVN)?
An interconnected membrane network supporting RNA virus replication.
28
How does poliovirus alter the host cell secretory pathway?
It hijacks ER exit sites (ERES) to form replication vesicles.
29
What cellular structure is repurposed for poliovirus replication?
The endoplasmic reticulum (ER).
30
What is the consequence of poliovirus-induced membrane modifications?
It disrupts normal protein trafficking and enhances viral replication.
31
What is the ERAD pathway, and how do coronaviruses exploit it?
The Endoplasmic Reticulum-Associated Degradation pathway, which is hijacked by coronaviruses to enhance replication.
32
What host proteins are affected by ERAD tuning in coronavirus infection?
EDEM1 and OS9, which are downregulated to favor viral replication.
33
How do coronaviruses modify the ERAD pathway?
They transform ER-derived vesicles into double-membrane structures housing viral replication complexes.
34
Where does hepatitis C virus (HCV) replication take place?
In a specialized ER-derived membranous web.
35
What viral proteins are involved in forming the membranous web?
NS5A, NS5B, and NS4B.
36
How do host lipids contribute to HCV replication?
Enrichment of cholesterol-rich lipid rafts facilitates viral RNA synthesis.
37
What are viral replication structures composed of?
Viral replication structures are composed of modified cellular membranes, viral proteins, and host factors.
38
How do viruses reorganise host membranes for replication?
Viruses reorganise host membranes by inducing membrane curvature, forming vesicles, and recruiting host lipids.
39
What role does the cytoskeleton play in virus replication?
The cytoskeleton provides structural support and helps transport viral components within the cell.
40
Why do viruses target organelles for replication?
Viruses target organelles to gain access to lipid membranes, enzymes, and other resources necessary for replication.
41
How do viruses benefit from modifying host organelles?
Modifying host organelles provides viruses with a protected environment and access to replication machinery.
42
Which host membranes are most commonly hijacked by RNA viruses?
Endoplasmic reticulum (ER), Golgi, mitochondria, and endosomes are the most commonly hijacked membranes.
43
What is the function of viral-induced double-membrane vesicles?
Double-membrane vesicles provide a protective environment for RNA replication and shield viral RNA from detection.
44
How do viral replication compartments shield RNA intermediates?
Replication compartments sequester viral dsRNA to prevent activation of host immune sensors.
45
What is the advantage of using membrane vesicles for viral replication?
Membrane vesicles concentrate replication factors and provide a scaffold for viral enzyme activity.
46
What is the significance of RNA virus replication occurring on membrane surfaces?
RNA virus replication on membrane surfaces allows efficient RNA synthesis and avoids detection.
47
How do viruses remodel endoplasmic reticulum membranes?
Viruses induce ER membrane curvature and vesiculation to create replication niches.
48
What is the role of autophagy-related pathways in virus replication?
Autophagy-related pathways provide membranes that some viruses repurpose for replication.
49
Why do some viruses manipulate lipid metabolism?
Lipid metabolism alterations ensure the production of membranes enriched in viral replication factors.
50
How do viral proteins interact with host lipids?
Viral proteins bind to and reorganise host lipids to enhance membrane curvature and vesicle formation.
51
What lipid modifications are essential for viral replication?
Phosphatidylinositol-4-phosphate (PI4P) and cholesterol-rich membranes are key for viral replication.
52
Which viral families are known for forming replication factories?
Flaviviruses, coronaviruses, picornaviruses, and hepatitis C virus all form replication factories.
53
What is the significance of replication factory size and shape?
Factory size and shape impact efficiency by controlling diffusion rates of replication components.
54
How do flaviviruses modify intracellular membranes?
Flaviviruses create a reticulovesicular network derived from ER membranes for replication.
55
What evidence supports the idea that viruses exploit the ER-Golgi system?
Viral replication depends on the ER-Golgi network for vesicle formation and trafficking.
56
Why do RNA viruses concentrate replication machinery in distinct compartments?
Concentrating replication machinery in compartments enhances efficiency and minimises host immune responses.
57
How do cryo-electron tomography and electron microscopy complement each other?
Cryo-electron tomography provides 3D images, while electron microscopy provides high-resolution 2D images.
58
What are the key differences between single-membrane and double-membrane replication structures?
Single-membrane structures are less protected, while double-membrane structures shield viral intermediates.
59
What role does viral RNA localisation play in replication efficiency?
RNA localisation in replication compartments ensures coordinated transcription and translation.
60
Why do viral RNA replication complexes require specific host proteins?
Host proteins stabilise viral RNA and support replication by providing essential cofactors.
61
What is a viral RNA synthesis compartment?
A viral RNA synthesis compartment is a microenvironment dedicated to viral genome replication.
62
What are spherules in viral replication?
Spherules are small vesicular invaginations used as replication compartments by some RNA viruses.
63
How do viruses create spherules?
Viruses create spherules by modifying host membranes and forming inward protrusions.
64
Which viruses are known to form spherules?
Flaviviruses, alphaviruses, and nodaviruses form spherules.
65
Why do spherules have a narrow neck connecting them to the cytoplasm?
The narrow neck allows controlled exchange of nucleotides and enzymes with the cytoplasm.
66
What is the role of viral proteases in replication structures?
Viral proteases cleave host and viral proteins to remodel replication structures.
67
How does hepatitis C virus manipulate lipid droplets?
HCV utilises lipid droplets as a source of membrane material for its replication complexes.
68
What is the function of phosphatidylinositol-4-phosphate in viral replication?
Phosphatidylinositol-4-phosphate (PI4P) is a key lipid for maintaining replication vesicle integrity.
69
What role do stress granules play in viral replication?
Stress granules sequester viral RNAs, but some viruses counteract this to facilitate replication.
70
How do viruses interact with host stress granules?
Viruses can inhibit stress granule formation or dissolve them to ensure efficient RNA translation.
71
What host factors are involved in coronavirus replication vesicle formation?
Coronavirus replication vesicles require host proteins involved in membrane trafficking.
72
How does poliovirus disrupt host cellular transport pathways?
Poliovirus hijacks the ER-Golgi network and disrupts protein secretion pathways.
73
What is the impact of viral replication factories on host cell function?
Replication factories alter host cell metabolism and interfere with normal cellular processes.
74
How do viruses evade immune detection within replication compartments?
Sequestering viral RNA in membrane-bound compartments reduces recognition by host sensors.
75
What mechanisms prevent the host cell from detecting viral dsRNA?
Viral dsRNA is hidden in vesicles, preventing activation of interferon pathways.
76
How does the replication structure of flaviviruses differ from that of coronaviruses?
Flaviviruses form invaginations within ER membranes, while coronaviruses form double-membrane vesicles.
77
What are convoluted membranes, and how do they contribute to viral replication?
Convoluted membranes (CMs) are disordered membranous structures associated with viral protein synthesis.
78
Why do some viruses form multi-vesicular bodies?
Some viruses form multi-vesicular bodies as part of their exit or replication strategy.
79
What host enzymes are required for viral membrane modifications?
Host lipid-modifying enzymes like PI4K and ACBD3 are crucial for replication membrane formation.
80
How does viral genome size influence replication compartment structure?
A larger viral genome may require more complex replication structures for organisation.
81
What role do mitochondria play in some viral replication strategies?
Mitochondria provide ATP and membrane surfaces for replication of some RNA viruses.
82
How do viruses exploit intracellular trafficking pathways?
Viruses exploit intracellular trafficking pathways to transport replication components efficiently.
83
What are the consequences of viral membrane modifications for cellular homeostasis?
Altering host membranes affects lipid balance, ER function, and protein secretion.
84
What is the significance of viral replication occurring near ER exit sites?
ER exit sites serve as hubs for viral RNA synthesis and vesicle formation.
85
Why do some viruses induce the formation of membrane tubules?
Viruses form membrane tubules to increase the surface area available for replication.
86
What is the role of the 'crown structure' in viral replication spherules?
The crown structure, formed by multimerized viral proteins (e.g., protein A in FHV), creates a channel through which newly synthesized viral RNA can exit the double-membrane vesicle into the cytoplasm.
87
How does poliovirus manipulate the ER-Golgi transport pathway to aid replication?
Poliovirus expresses 3A protein, which binds GBF1 and interferes with COPI-mediated recycling, hijacking PI4KIIIβ to produce PI4P-enriched membranes that recruit viral RNA polymerase and form replication vesicles.
88
How do coronaviruses exploit the ERAD pathway for replication vesicle formation?
Coronaviruses hijack ERAD tuning by incorporating ERAD components (e.g., EDEM1, OS-9, SEL1L) into vesicles. These vesicles, instead of being degraded by autophagy, are repurposed into double-membrane replication compartments.
89
What is the function of NS5A in hepatitis C virus replication?
NS5A is a multifunctional viral protein that interacts with host PI4KIIIα to alter lipid composition of ER membranes, facilitating formation of the membranous web and recruitment of the NS5B polymerase for RNA replication.
90
What is focused ion beam (FIB) milling and how is it used in virology?
FIB milling shaves away thin slices of whole cells, allowing 3D reconstruction of viral replication organelles via cryo-electron tomography, providing atomic-level insight into virus-cell interactions.
91
Why do viruses form double-membrane vesicles (DMVs) for replication?
DMVs concentrate viral components, protect replication intermediates like dsRNA from host immunity, and provide controlled environments for efficient and temporally regulated genome replication.
92
What are the benefits of using Flock House Virus (FHV) as a model for RNA virus replication?
FHV has a simple genome encoding only four proteins, replicates on mitochondrial membranes, and forms clearly defined replication spherules that are ideal for structural and biochemical studies.
93
How do RNA viruses manipulate host lipid metabolism to form replication structures?
RNA viruses recruit lipid-modifying enzymes like PI4K to enrich membranes with specific lipids (e.g., PI4P), promoting curvature, vesicle formation, and anchoring of replication complexes.
94
What are the functional similarities between replication factories of different positive-sense RNA viruses?
Despite using different host pathways and organelles, replication factories commonly feature membrane rearrangements, RNA-enclosing vesicles, viral protein crowns, and lipid modifications.
95
How does cryo-electron tomography enhance the study of viral replication organelles?
Cryo-ET provides 3D visualization of intracellular structures at near-native conditions and high resolution, revealing the organization, topology, and dynamic changes of viral replication compartments.
