Full Test Collection 1 Flashcards
How is the innate immune system activated?
The innate immune system is activated by the binding of PAMPs/MAMPs to receptors that can activate the innate immune response.
What are PAMPs/MAMPs?
PAMPs are pathogen-associated molecular patterns and MAMPs are microbial-associated molecular patterns. They can be recognised by receptors of the innate immune system. PAMPs and MAMPs are common to pathogens and microbes, but are absent or sequestered in the host.
How do bacteria defend themselves against viruses?
Bacteria defend themselves from viruses using intracellular proteins called restriction factors, which block viral propagation.
What is the first barrier for pathogens in vertebrates, and how does this barrier defend the host against pathogens?
The epithelial surfaces that form the skin and line the respiratory, digestive, urinary, and reproductive tracts. The epithelia provide both physical and chemical barriers to invasion of pathogens: tight junctions between epithelial cells bar entry between the cells (e.g. keratinised epithelial cells), and a variety of substances secreted by the cells discourage the attachment and entry of pathogens (e.g. sebaceous glands that secrete fatty acids and lactic acids which inhibit bacterial growth). Epithelial cells in all tissues, including those in plants and vertebrates, secrete antimicrobial molecules called defensins. Defensins are positively charged, amphipathic peptides that bind to and disrupt the membranes of many pathogens, including enveloped viruses, bacteria, fungi, and parasites. The epithelial cells that line internal organs such as the respiratory and digestive tract also secrete slimy mucus, which sticks to the epithelial surface and makes it difficult for pathogens to adhere. The beating of cilia on the surface of the epithelial cells lining the respiratory tract and the peristaltic action of the intestine also discourage the adherence of pathogens. Moreover, healthy skin and gut are inhabited by enormous numbers of harmless and often helpful commensal microbes, collectively called the normal flora, which compete for nutrients with pathogens; some also produce antimicrobial peptides that actively inhibit pathogens proliferation.
Which receptors recognise PAMPs?
Pattern recognition receptors (PRRs).
Where are PRRs located, and give an example of its function in that location.
PRRs can be transmembrane proteins and located on the surface of many types of host cells where they recognise extracellular pathogens. For example, on macrophages and neutrophils they can mediate the uptake of pathogens into phagosomes to destroy the pathogens. PRRs can also be located intracellularly, where they can detect intracellular pathogens such as viruses. These PRRs are either free in the cytosol or associated with the membranes of the endolysosomal system.
Which types of PRRs are present in mammals, where are they located, and what do they recognise?
Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-like receptors (RLRs), and C-type lectin receptors (CLRs).
TLRs are transmembrane cell-surface receptors and recognise distinct ligands of various pathogens (e.g. TLR4 recognises LPS and TLR5 recognises flaggelin). NLRs are solely cytoplasmic and recognise a distinct set of bacterial molecules. RLRs are solely cytoplasmic and detect viral pathogens. CLRs are transmembrane cell-surface proteins and recognise carbohydrates on various microbes.
Name examples of important pro-inflammatory cytokines.
Tumour necrosis factor-a (TNFa), interferon-y (IFNy), a variety of chemokines, and various interleukins (e.g. IL1, IL6, IL12, and IL17).
What is the difference between macrophages and neutrophils?
Macrophages are long-lived phagocytes that reside in most vertebrate tissues. Macrophages are among the first cells to encounter invading microbes, whose PAMPs activate the macrophages to secrete pro-inflammatory signal molecules. Neutrophils are short-lived phagocytes that are abundant in blood, but are not present in healthy tissues. They are rapidly recruited to sites of infection by various attractive molecules, including chemokines secreted by activated macrophages and peptide fragments produced from cleaved, activated complement proteins. Recruited neutrophils contribute their own pro-inflammatory cytokines.
What happens if a pathogen is too large to be phagocytosed by phagocytic cells?
Instead of phagocytosing the pathogen, phagocytic cells like macrophages, neutrophils, and eosinophils will gather around the invader. They secrete defensins and other damaging agents and release the toxic products of the respiratory burst. This barrage is often sufficient to destroy the pathogen.
What does the complement system entail?
The complement systems consists of about thirty interacting soluble proteins that are mainly made continuously by the liver and are inactive until an infection or another trigger activates them. These proteins amplify and complement the action of antibodies made by B cells, but some are also secreted PRRs, which directly recognise PAMPs on microbes.
Which viral PAMPs can PRRs recognise? And by which PRRs are they recognised?
Elements of the viral genome like double-stranded RNA (dsRNA), which is recognised by TLR3, and CpG motifs that are recognised by TLR9.
What happens when mammalian PRRs sense viral dsRNA?
When mammalian PRRs sense viral dsRNA, they induce the host cell to produce and secrete two antiviral cytokines, the type 1 interferons interferon-a and interferon-b.
How do type 1 interferons function?
Type I interferons act in both an autocrine fashion on the infected cells that produced it and a paracrine fashion on uninfected neighbours. They bind to a common cell-surface receptor, which activates the JAK-STAT intracellular signalling pathway to stimulate specific gene transcription and thereby the production of more than 300 proteins, including many cytokines.
How do type 1 interferons block viral replication?
They activate a latent ribonuclease that non-specifically degrades single-stranded RNA. They also indirectly activate a protein kinase that phosphorylates and inactivates the protein synthesis in the infected host cell. If these measures fail, the cell undergoes apoptosis to prevent viral replication.
What is the function of natural killer (NK) cells?
NK cells, which can be enhanced by type 1 interferons (interferon-a and interferon-b) are recruited to the site of inflammation and destroy virus-infected cells by inducing apoptosis.
How do natural killer (NK) cells recognise virus-infected cells?
NK cells recognise special cell-surface proteins called major histocompatibility complex 1 (MHC 1) proteins. NK cells have cell-surface inhibitory receptors that monitor MHC1 levels: normal healthy cells have a high level of MHC1, which bind to the inhibitory receptors of NK cells and inhibits apoptosis. Virus-infected cells display a low MHC1 level, so the inhibitory receptors are not blocked and can induce apoptosis in virus-infected cells. NK cell killing activity is stimulated when various activating receptors on the NK cell surface recognise specific proteins that are greatly increased on the surface of virus-infected cells and some cancer cells.
Explain how the evasion of cytotoxic T-cells by virus-infected cells leads to apoptosis by natural killer (NK) cells.
To escape death by cytotoxic T-cells, viruses inhibit MHC gene expression or they block the intracellular assembly of MHC complexes. However, by doing this the level of MHC in a cell decreases, resulting in the cell being killed by NK cell-induced apoptosis. Moreover, a lot of recognisable cell surface proteins are expressed on the cell surface, resulting in NK cells regonising these virus-infected cells.
Explain how dendritic cells can activate the adaptive immune system.
Dendritic cells can recognise pathogens by their PAMPs, and can subsequently phagocytose them. By doing this, they become activated. Activated dendritic cells can cleave proteins made by pathogens into peptide fragments, allowing them to bind to new MHC complexes, which can then carry the fragments to the dendritic cell surface. The cells can then migrate to a nearby lymphoid organ, such as the lymph nodes, where they present the peptide-MHC complex to T cells that then get activated.
Which proteins act as central components in the complement system?
Complement proteins C1 to C9, the PRR mannose-binding lectin (MBL), MBL-associated serine protease (MASP), and factors B and D.
Explain the signalling cascade in the complement system and its outcomes.
Through the classical pathway (antibody binding), lectin pathway (mannose binding), and the alternative pathway (molecules on pathogen surfaces), a proteolytic cascade of the central components of the complement system, the complement protein C3 is cleaved. The small fragment of C3, called C3a, promote an inflammatory response by recruiting leukocytes to the site of infection. The larger fragment of C3, called C3b, binds covalently to the surface of the pathogen. Membrane-immobilised C3b triggers a further cascade of reactions that leads to the assembly of membrane attack complexes by the complement proteins C5 to C9. These protein complexes assemble near the site of C3 activation, forming aqueous pores through the membrane. For this reason, and because they perturb the structure of the lipid bilayer in their vicinity, they make the membrane leaky and can, in some cases, cause the microbe to lyse. C3b-binding receptors on phagocytic cells also enhance the ability of these cells to phagocytose a pathogen, and similar receptors on B cells enhance the ability of these cells to make antibodies against various microbial molecules on C3b-coated pathogens. Due to the effective destructiveness of the complement system, it must be rapidly inactivated as well. This is done in at least two ways. First, specific inhibitor proteins in the blood or on the surface of host cells terminate the cascade, by either binding or cleaving complement components once the components have been activated by proteolytic cleavage. Second, many of the activated components in the cascade are unstable; unless they bind immediately to either the next component in the complement cascade or to a nearby membrane, they rapidly inactivate.
How does the host protect itself against the complement system?
Cells produce sialic acid. Because pathogens generally lack sialic acid, they are singled out for complement-mediated destruction, while host cells are spared. However, some pathogens like Neisseria gonorrhoeae coat themselves in sialic acid, resulting in evasion of the complement system.
Explain how a Mycobacterium tuberculosis infection can result in pyroptosis.
When Mtb escapes the phagosome, for example by using the type 7 secretion system ESX1 to damage the phagosomal membrane, it ends up in the cytoplasm. In the cytoplasm, ESX1 also forms pores in the plasma membrane, resulting in a K+ efflux that activates NLRP3. Subsequently, NLRP3 forms an inflammasome with pro-caspase-1 and ASC. Caspase-1 can then cleave itself, and form active caspase-1 which can cleave pro-IL-1B and pro-IL-18. Caspase-1 also cleaves pro-Gasdermin-D to form active Gasdermin-D, which can form pores that lead to pyroptosis. IL-1B and IL-18 use these pores to perform their function around neighbouring cells.
How can a macrophage avoid pyroptosis?
A machinery called ESCRT can repair both the phagosomal membrane as the plasma membrane, resulting in Mtb not being able to escape the phagosome, or the macrophage not undergoing Mtb-induced pyroptosis due to avoiding a K+ efflux.
What is the difference between the canonical and non-canonical activation of inflammasomes?
With the canonical activation of an inflammasome, the recognition of a PAMP results in the transcription of inflammasome components (e.g. NLRP3, ASC, pro-caspase-1, pro-IL-1B, and pro-IL-18). After this first signal, pathogens have to escape the phagosome and end up in the cytosol to activate the NLRP3 inflammasome by damaging the plasma membrane, resulting in a K+-efflux. After this second signal, the inflammasome can be activated, caspase-1 becomes activated, and cleaves pro-IL-1B, pro-IL-18, and pro-Gasdermin-D. Active Gasdermin-D forms pores in the membrane, which results in pyroptosis and the ability of the IL-1B and IL-18 to migrate through these pores and function at neighbouring cells. With non-canonical activation of the inflammasome, the PAMP LPS is directly sensed by the human pro-caspase-4/5, which become activated and can cleave pro-Gasdermin-D to form active Gasdermin-D, which forms pores in the membrane, which results in pyroptosis.
Name the two forms of autophagy.
The two forms of autophagy are the canonical xenophagy and the non-canonical LC3-associated phagocytosis (LAP).
What machinery is required for LAP?
The LC3-lipidation machinery, the Atg5-12-16L1 complex, the protein Rubicon, and the generation of reactive oxygen species (ROS) by the NADPH oxidase.
What machinery is required for xenophagy?
The ULK1 complex, the Atg5-12-16L1 complex, and LC3-II.
How does Mycobacterium tuberculosis damage the phagosomal membrane and enter the cytosol?
By using the coordinated action of the ESX-1 Type 7 secretion system (T7SS).
What is the function of ATG7 and ATG14?
ATG14 has a function in regulating fusion of autophagosomes containing Mycobacterium tuberculosis with lysosomes, and also has a function in the endosomal pathway that is autophagy-independent. Both ATG7 and ATG14 control the replication of cytosolic bacteria through either recapture of bacteria from the cytosol or sealing of damaged phagosomes by autophagosomes as reported for Salmonella. ATG7 and ATG14 are required to control Mtb infection.
What does autophagy entail?
Autophagy, which can be called the “housekeeping system”, entails the sequestration of cargo in a double membrane vesicle.
What is xenophagy? How does it function?
Xenophagy is the autophagy of microbial invaders. Xenophagy functions in the direct elimination of invaders, activation of immune responses, inflammasome control, and antigen presentation.
Give the pathway of xenophagy. How does this compare to viral phagocytosis?
In xenophagy, phagocytic cells engulf a pathogen, and the pathogen is sequestered in a double membrane vesicle named the autophagosome. Subsequently, the autophagosome is fused with a lysosome containing antimicrobial toxins, and the pathogen is degraded in this autolysosome. In xenophagy with viral pathogens, a virus is engulfed by a phagocytic cell and viral nucleic acids are then sequestered in an autophagosome. The autophagosome containing viral nucleic acid is then turned into an endosome and the viral nucleic acid can be recognised to induce expression of type 1 interferons (interferon-a and interferon-B).
Which factors induce autophagy?
Microbial invaders, low energy, and nutrient limitation.
Is autophagy always host-protective?
No, autophagy can be host-protective by delivering pathogens to lysosomal degradation. However, several pathogens subvert or hijack autophagy to facilitate replication and spreading (e.g. the poliovirus, a nonlytic virus which spreads by autophagy-mediated secretion pathways).
Give the pathway of autophagosome maturation.
In autophagy, due to an infection or due to low energy or nutrient limitation, a double membrane isolation membrane is formed, which recruits the protein LC3. LC3 can be present in two forms: in the cytosol it is called LC3-I, and when it is lipidated and is able to conjugate to the autophagosome membrane, it is called LC3-II. After the double membrane isolation membrane is formed, the isolation membrane elongates, LC3-II is recruited to the membrane, and cargo (pathogens, mitochondria, etc.) is recruited. This state of the isolation membrane is called the phagophore. After completion of the phagophore, it is called an autophagosome and it can fuse with a lysosome to form an autolysosome, which degrades the cargo inside.
How do selective autophagy receptors (SLRs) function in xenophagy.
Salmonella can escape phagocytosis and end up in the cytosol, after which it is recognised by the ubiquitin machinery, after which the bacterium can be sequestered in an autophagosome and lysed. SLRs, like Atg8, recognise ubiquitin and/or galectins on bacteria or damaged phagosomes and target them to LC3-II. SLRs also deliver neo-antimicrobial peptides derived from ubiquitinated proteins. These ubiquitinated proteins are often useful precursors for new antimicrobial peptides. These neo-antimicrobial peptides and the ubiquitinated pathogen end up in the same autophagosome, where the antimicrobial peptides can degrade the pathogen.
Give the pathway of LC3-associated phagocytosis (LAP).
With LC3-associated phagocytosis (LAP), the cell membrane engulfs a pathogen in just a single membrane (unlike the double membrane vesicles of xenophagy). This single membrane vesicle also recruits the LC3 protein, but only after undergoing a respiratory burst of reactive oxygen species (ROS). Then, this single membrane isolation vesicle is called a LAPosome. The protein Rubicon induces LC3-associated phagocytosis and inhibits xenophagy. Afterwards, a LAPosome can fuse with a lysosome to form a phagolysosome.
Why is it important that both xenophagy and LAP can occur in cells?
Both pathways of xenophagy and LAP are very important, because, for example, xenophagy is protective against Staphylococcus aureus infection, but LAP provides a replication niche for Staphylococcus aureus in neutrophils. So, enhancing autophagy might be useful for infections of Salmonella, but are detrimental for infections of Staphylococcus aureus, where LAP provides a replication niche and thus LAP should be inhibited to provide host resistance.
What is Persephone and how is it activated?
Persephone is a serine protease that belongs to a danger pathway activated by abnormal proteolytic activities, and results in the activation of the Toll pathway. The Persephone pathway can be activated by the exogenous proteases of a range of different microorganisms, including Gram-negative bacteria. Persephone itself is an immune receptor able to sense a broad range of microbes through virulence factor activities rather than molecular patterns.
Explain the Persephone signalling cascade.
Persephone has a unique region in the pro-domain of Persephone that functions as bait for exogenous proteases independently of their origin, type, or specificity. Cleavage in this bait region constitutes the first step of a sequential activation and licenses the subsequent maturation of Persephone to the endogenous cysteine cathepsin 266-29-p. Activated Persephone is then able to activate the Spaetzle-processing enzyme (SPE), after which activated SPE activates pro-Spaetzle to form active Spaetzle, which triggers the Toll pathway.
Explain Ca2+ levels in a normal situation and how it can lead to toxicity, growth inhibition, and defence responses.
The extracellular Ca2+ concentration is several magnitudes higher than intracellular Ca2+ concentration, resulting in the plant being at risk for a Ca2+ overload. Whereas low extracellular Ca2+ concentrations only prompt transient intracellular Ca2+ concentration changes, sustained elevation occurs beyond a threshold, causing toxicity, growth inhibition, and defence responses.
What are ACAs and CAXs and what do they do?
Ca2+-ATPases (ACAs) and Ca2+/H+-exchangers (CAXs) are proteins that are thought to function in maintaining a low resting intracellular Ca2+ concentration in plants. CAXs also coordinate with ACAs to control plant fitness and immunity under specific conditions, although this mechanisms remains unclear.
What does a plant do to cope with fluctuating extracellular Ca2+ concentrations?
Vacuolar Ca2+ sequestration mediated by CAX1/3.
