IMI6: Immune response to intracellular pathogens Flashcards
What are the two main classes of intracellular microbes?
Obligate intracellular pathogens
Facultative intracellular pathogens
What are facultative intracellular pathogens?
can survive and proliferate outside the host cell, and can invade cells – this allows bacteria or parasites to cross cells and survive in phagosomes
What are obligate intracellular pathogens?
Cannot reproduce outside the host cell as their proliferation and biosynthetic pathways depend on the energy metabolism of the host cell. They generally have inactive extracellular forms to be passed between cells or organisms.
What are the inactive extracellular forms of obligate intracellular pathogens that have low metabolic activity?
Viral particles
Bacterial spores
Encapsulated cells
Give examples of diseases caused by intracellular pathogens
Tuberculosis, listeriosis, flu and herpes: often have strategies to colonise macrophages to avoid phagocytosis
What are the first two steps of the immune response against intracellular pathogens?
1) The body needs to realise (detect) that a pathogen is there to be dealt with.
2) The body needs to destroy (or inactivate) the pathogen once it has been found.
What are the three main characteristics of viruses that define what immune responses will be effective at sensing and/or targeting the virus?
1) What nucleic acid their genome is made of (DNA or RNA; single or double stranded)
2) Whether or not they have a lipid envelope
3) Whether they replicate their genome in the cytoplasm or the nucleus
How can intracellular pathogens in endosomes be detected?
there is evidence that cell-membrane TLRs can be endocytosed and expressed on the vesicles
What is a virion made up of?
nucleic acid genome (RNA or DNA) surrounded by a capsid which is a protective protein shell. Some viruses may also have an extra layer of protection in the form of an envelope which is a lipid bilayer around the capsid.
What is a virus classified by?
Type of nucleic acid in their genome
Presence of an envelope
What are the 7 groups of viruses?
Group I – dsDNA Virus Group II – ssDNA virus Group III – dsRNA virus Group IV – positive sense ssRNA virus Group V – negative sense ssRNA virus Group VI – retroviruses (DNA via RNA) Group VII – DNA/RNA hybrid virus
What is the first step of entry of a virus into a cell common to all viruses?
It attaches itself to the cell surface via a glycoprotein on the viral surface and a specific receptor on the cell
Following binding of a viral glycoprotein to a specific cell receptor, what are the two modes of entry for a virus?
Endocytic route
Non-endocytic route
Describe the endocytic route of entry for a virus
non-enveloped virus triggers its clathrin-mediated endocytosis and escapes the endosome before it becomes a lysosome
Describe the non-endocytic route of entry for a virus
enveloped virus has viral glycoproteins which cause the viral membrane to fuse with the cell membrane, allowing the capsid to enter the cytosol
Where do RNA viruses especially those with +ve ssRNA, localise generally? why? (give an exception)
Within the cytosol where their genomes can be translated by ribosomes
Flu viruses are RNA viruses localised in the nucleus
Where do Retroviruses and DNA viruses generally localise? (give an exception)
nucleus
poxviruses are DNA viruses localised in the cytoplasm
What does - or + RNA mean?
+ stranded RNA can be directly translated into protein by the ribsosome whereas - stranded or double stranded genomes need to be transcribed first
What largely defines what cells viruses can infect?
which cell type(s) the receptor is found on (and which it is missing from)
What type of genome does Herpes Simplex virus have?
dsDNA genome: whose capsid releases the genome into the host nucleus.
Explain how herpes simplex virus hyjacks the replication mechanism of cells, before being released from the cell
The viral DNA circularises and its early Genes are transcribed into early mRNA which is translated in the cytoplasm into early proteins. The early proteins are required for viral replication, so re-enter the nucleus. Late genes are then transcribed into late mRNA which encodes late proteins that form the capsid and envelope (produced in ER and incorporated into nuclear membrane). These re-enter the nucleus, where the viral DNA replicates using the ‘rolling circle’ model. Individual genomes are cut and repackaged into a capsid, which fuses with the nuclear membrane and ‘buds-off’ to become surrounded by an envelope. This virus then moves through the ER, and buds-off again to undergo exocytosis to become released from the cell.
In the case of an adenovirus infection, how many antibodies are found on viral glycoproteins?
very few
Upon entry into the cell, the antibodies on the viral surface are bound by an intracellular antibody receptor, what is this called?
TRIM21
What does antibody binding to TRIM21 do?
It promotes the formation of polyubiquitin chains which recruit the proteasome, which degrades viral proteins into short peptides and disrupts the virus’ structure.
Where are short peptides (from degraded viral proteins) presented? To what affect does this have?
MHC I
- viral DNA is left naked in the cytoplasm and acts as a potent PAMP and alerts the cell of infection
Why are enveloped viruses not detected via MCH I?
Their surface proteins are left on the cell membrane when they enter the cell, therefore their viral surface cannot be detected by antibodies
What is DNA in the wrong cellular compartment recognised by?
cyclic GMP/AMP synthase (cGAS)
What does recognition of DNA in the wrong cellular compartment by cyclic GMP/AMP synthase (cGAS), lead to the production of?
cGAMP as a second messenger
What does cGAMP as a second messenger bind to?
STING on the ER membrane which causes the activation of the kinase TBK1
What does TBK1 activate? What does this do?
IRF3, enters the nucleus and activates transcription factors of type 1 interferons such as IFN-a and IFN-b
What can cGAS DNA sensing also be used to detect? How is this theorised to have happened?
Intracellular bacteria, which have been theorised to generate cyclic dinucleotides which can bind to and activate STING (as STING on the ER membrane which causes the activation of the kinase TBK1, which activates IRF3, which enters the nucleus and activates transcription factors)
What is cGAS DNA sensing is also important for?
Detecting other threats to cellular health such as mitochondrial integrity, DNA damage and errors in cell division
How can the cell’s normal mRNA be distinguished from viral RNA by PRRs?
The sensing proteins are RLRs and include:
- RIG-I – senses <4000nt RNAs that have triphosphates at their 5’ end in the nucleus and cytoplasm. They will not sense mRNAs due to their 5’-cap.
- MDA5 – senses >2000nt dsRNA which is produced during viral replication, cells do not replicate RNA so this is indicative of viral infection.
What does RLR stand for?
RIG-I-like receptor
What do RIG-I and MDA5 associate with?
mitochondrial antiviral signalling proteins (MAVS)
Multiple MAVS signal through what? Which in turn activates what?
IRF3 which activates IFN-a and IFN-b
What are the three IFN classes?
- Type I IFN (12 a-subtypes and IFN-b) – respond to pathogen induced signals
- Type II IFN (IFN-g) – produced by activated immune cells to signal to other immune cells
- Type III IFN (3 l-subtypes) – lead to an antiviral state in infected cells and structurally related to IL-10
What does IFN stand for?
Interferon
What does IFN signalling activate and attract, in order to turn on IFN-stimulated genes (ISGs)
Immune cells and activates IRF7 in non-immune cells to turn on IFN-stimulated genes (ISGs) to place the cell in an antiviral state
What does ISGs stand for?
IFN-stimulated genes
What do ISGs include?
Antiviral PRRs and restriction factors
What are restriction factors?
Restriction factors are cellular gene products which prevent specific pathogen functions and they are the most rapidly evolving genes in the genome
How does INF signalling make it more difficult for the pathogens to spread?
Warns nearby cells of viral infections
How do cytotoxic T-cells become activated?
Cytotoxic T cells with the correct TCR sense loaded MHC I and become activated and proliferate to be able to directly act on infected cells.
What are the innate cells that deal with intracellular pathogens? How?
NKC: They provide an early source of cytokines and chemokines until specific T-cells are activated
What do NK cells produce to activate macrophages and promote phagocytosis?
IFN-gamma
What do cytotoxic cells produce to lyse infected host cells?
cytotoxic granules, perforin and granzymes
How is the significance of NK cell response to viral infections known?
individuals with T and B cell deficiencies can control major viral infections, but those with NK cell deficiencies are susceptible to certain viral infections
What does NK activation depend on?
The balance between inhibitory receptors and activating receptors
How are healthy cells are tolerated by NK activation?
More inhibitory receptors are ligated to the MHC I than activating receptors
How do NK cells know to kill tumour cells?
They are missing MHC I, therefore no inhibitory MHC I is bound
How is the destruction of viral cells initiated by NK cells
There is an upregulation of activating receptors to overwhelm inhibitory receptors, in response to intracellular stress signals, leading to destruction of the cell. However, activating ligands are still not identified.
Define what an acute viral infection is
A short duration and fast recovery time
When can acute viral infections not dealt with efficiently?
In an
- Immunocompromised individuals
- Immunopathology as the virus causes a cytokine storm
What are the glycoproteins on the influenza virus surface?
haemagglutinin and neuraminidase
What normally happens to the glycoproteins on the surface of influenza virus?
Neutralised by antibodies
Describe the antigenic drift phenomenon
The sequence of these viral glycoproteins can be changed which allows the virus to repeatedly infect the same individual
When does antigenic shift occur?
When flu viruses from different animals infect the same cell and swap parts of their genome to form a novel combination of properties.
How does influenza evade the innate immune system?
By encoding the NS1 gene which prevents the activation of RIG-I by ubiquitination from TRIM25 signalling
What does the NS1 gene do?
It prevents the activation of RIG-I by ubiquitination from TRIM25 signalling. RIG-I can, therefore, not signal to MAVS. NS1 also inhibits PKR (another dsRNA sensor) which is an ISG that can be activate when nearby cells are infected
Define chronic viral infections
Infect the host over a long-term, even a lifetime
Give an example of a chronic viral infection, how does it make itself chronic?
Herpes simplex 1 virus (HSV): which establishes a latent infection by escaping detection and entering an inactive state
Where does the HSV genome reside during their latent cycle?
In neurons
How can HSV move through a population silently?
Through asymptomatic shedding whereby it is present in saliva and genital secretions without displaying other symptoms
Why do proteins not get translated for viruses in the latent cycle?
They only transcribe latency-associated RNA transcripts (LAT) which do not get translated into protein
How do viruses in the latency cycle evade detection by the innate immune system?
1) Only LAT transcribed, therefore no protein translated. This means there is no protein presented on MHC I, allowing the virus to evade immune detection
2) By hiding in the neurons, HSV is far away from the HSV undergoing the lytic cycle in the epithelial cells, away from IFN signalling
What is ICP0?
An immune evasion gene the HSV produces, it disrupts promyelocytic bodies (PML) which silence nuclear DNA viruses
Give an example of bacteria that cannot be detected in cells by antibody/TRIM21?
bacteria such as tuberculosis that live and reproduce in endosomes do not enter the cytoplasm, so are not exposed to TRIM21.
What biological process is mediated by pyrin domains?
Pyrin domains facilitate the formation of inflammasomes
Which cells have MHC II?
Only APCs
Can you remember which class(es) of T cells recognise MHC Class I-bound peptides?
CD8+ TH2
Cytotoxic T cells (CTL)
How many HA and NA subtype populations are there in inluenza?
19 HA
9 NA
What are the four most important immune cells/actions for dealing with intracellular pathogens?
- MCH class I antigen presentation
- NK cells
- Intracellular PRRs
- Cytotoxic T cells
How can HSV evade extracellular immune molecules?
Its viral glycoprotein (gC) can bind to C3b to prevent it binding other complement proteins.
HSV is enveloped, so what is it susceptible to?
MAC and opsonisation of the virus or infected cell
How are intracellular bacteria protected from the extracellular humoral response and cytoplasmic sensors
By living in endosomes and intracellular vesicles
Which bacteria can thrive in macrophage phagosomes?
M.tuberculosis, L.typhimurium, and E.coli
What is Lysteria Monocytogenes?
A bacterium associated with food poisoning that replicates and spreads from the cytoplasm
Where does Lysteria Monocytogenes colonise?
Peyer’s patches (in particular the goblet cells)
How does Lysteria Monocytogenes cross the gut-barrier?
Using bacterial internalin interacting with E-cadherin
How does Lysteria Monocytogenes make its way into the lamina propria?
It is transcytosed
It can cross the blood-brain barrier and placental barriers as well
What does L. Monocytogenes release to create pores in the cell membrane that disrupts intracellular processes, and promotes bacterial entry?
LLO
What effect does LLO have on the cell?
It alters ion balance of the cell, and leads to mitochondrial fission due to over abundance of Ca2+. This is beneficial for bacterial infection
How is SUMOylation disrupted by LLO?
SUMOylation is also disrupted through the degradation of UBC9 in response to LLO.
What does LLO do to histone phosphorylation and immune genes?
It also disrupts histone phosphorylation and interferes with gene expression of genes involved in immune responses.
Once L. Monocytogenes is internalised in the cell, what does it secrete? To what affect?
It secretes LLO and phospholipases to degrade the internalisation vacuole
Once L. Monocytogenes is internalised in the cell, how does it act?
It then modifies its surface and produces virulence factors that compromise distinct cellular functions.
What is LNTA and what does it do?
A virulence factor that compromises distinct cellular functions by binding to BAHD-1 to repress its function and cause the expression of ISGs.
What is BAHD-1?
Heterochromatin protein that acts as a transcription repressor and has the ability to promote the formation of large heterochromatic domains
What does L. Monocytogenes do to one of its poles? To what effect?
Covers it with ActA which recruits small actin filaments that rapidly grow to form comet tails to facilitate bacterial movement. This allows it to push the cell membrane into a neighbouring cell, and colonise it as well.
