Chapter 3 Vol II: The Early Host Response

The Early Host Response Introduction • • • • These defenses perform one of several possible functions: protecting the cell: thwarting virus reproduction; or triggering rapid cell death, thereby eliminating a virus factory Once the infection is resolved or controlled, memory of the event is established; memory T and B cells are rapidly reactivated if that same .Immune pathogen is encountered again later in life Responses macrophages The first critical moments: how do individual cells detect a virus neutrophils T cells infection? B cells A viral infection in a host can begin only once physical and chemical barriers are breached and virus particles encounter living cells that are both susceptible and permissive The importance of an early and appropriate response cannot be overstated: if the response is delayed or weak, the host may die from the consequences of unrestricted spread of the virus Such processes are termed intrinsic cellular defenses to distinguish them from the defenses possessed by specialized cells of the innate and adaptive arms of the immune system The immediate response to an infection is based on two coupled processes: detection and alarm Once a microbe has been detected, the infected cell must then initiate the series of events that lead to an appropriate defense Cell signaling induced by viral entry receptor engagement Many transmembrane proteins present on the cell surface are linked to intracellular molecules, such that binding of the "normal" ligand triggers pathways that enable the cell to respond to changes in its environment Thus, even before the virus enters the cell, the dynamics of ion flow, membrane permeability, protein localization within the cytoplasm, and host gene transcription may change Anatomical and chemical barriers Intrinsic Innate immunity Acquired immunity When these barriers are penetrated, additional host defenses, including intrinsic and innate defenses, come into play to contain the infection Receptor-mediated recognition of microbe-associated molecular patterns A second way that cells respond to infection is by recognition of structural features that are unique to the pathogen by host "detector" proteins Recognition of PAMPs or DAMPs by pattern recognition receptors rapidly triggers the synthesis of antimicrobial products, mobilization of immune cells to lymph nodes, and immune cell activation Specialized bacterial Four types of pattern recognition receptors are amongst and fungal the best-studied: toll-like receptors (TLRs), nucleotidecarbohydrates binding oligomerization domain-like receptors (NLRs), c-type Atypical forms of lectin receptors (CLRs),and RIG-I-like receptors (RLRs) nucleic acids Toll-like receptors (TLRs) Microbe-specific TLRs are type I transmembrane proteins that are polypeptides conserved from sea urchins to humans, and that are Unusual metabolites able to recognize both intracellular and extracellular microbial ligands TLRs 1, 2, 4, 5, and 6 are transmembrane proteins embedded in the plasma membrane; they recognize primarily extracellular microbes, such as bacteria, fungi, and Protozoa, although the coat proteins of some viruses can be detected by these cell surface molecules TLRs 3, 7, 8, and 9 are present within endocytic compartments of the cell and recognize primarily nucleic acid PAMPs derived from viruses or intracellular bacteria After ligand binding, the TLRs, like many receptors, aggregate in the plasma or endosomal membrane, an event that stimulates binding of adapter proteins, including protein kinases, that for the amplify the signal, leading to the first step in the inflammatory response All TLRs, with the exception of TLR3, engage MyD88; TLR3 interacts only with TRIF to stimulate IRF3 and NF-kB In addition, naturally occurring mutations of human TLR genes are associated with an inability to control many bacterial infections, as well as increased central nervous system disease following herpes simplex virus infections RIG-I-Like Receptors (RLRs) An obstacle for cellular detection of viruses is that these obligate intracellular parasites are made of the same basic building materials as the cell itself Unlike the TLRs, RLRs are present in all cells; hence, virtually any cell in the body can use the RLR detection system to sound the alarm upon viral infection Once engaged, RIG-I or MDA5 bind to a protein associated with mitochondrial membranes, called MAVS (mitochondrial antiviral signaling protein), to induce pathways that lead to the production of type I IFNs RIG-I recognizes short RNA ligands with a 5' phosphate group, which is common in viral RNAs and distinguishable from the 5' cap structures present on all cellular mRNAs Cytoplasmic DNA sensors DNA is normally nuclear; thus, the presence of DNA in the cytoplasm is a danger signal, indicative of either infection or nuclear disintegration, as found in some cancers Upon binding DNA, the protein cGAS (cyclic GMP-AMP synthase) catalyzes the reaction of GTP and ATP to form cyclic GMP-AMP (cGAMP) cGAMP binds to STING (stimulator of interferon genes), which triggers phosphorylation of IRF3 Activated IRF3 then enters the nucleus to drive transcription Viral proteins antagonize pattern recognition receptors Clearly, viral gene products can bypass or modulate the intracellular detectors of infection to enable the viral genome to be maintained in a host population The importance of inhibiting this fundamental first step in immunity has caused some to question whether viral oncoproteins were selected for their nimbleness Pathogen-associated molecular patterns • • • • in antagonizing pattern recognition rather than their ability to drive cell proliferation Cell-Intrinsic Defenses Apoptosis (programmed cell death) Such programmed cell death continues throughout life: every day in an adult human, 50 billion to 70 billion Vocab cells die by apoptosis Apoptosis: a normal Apoptotic cell death is the result of a cascade of biological process used intracellular reactions that eventually leads to chiefly to eliminate nuclear membrane breakdown, chromatin particular cells during condensation, loss of membrane integrity (called development and "blabbing," in which bubbles of cytoplasm appear on differentiation and to the cell surface), and eventually DNA degradation maintain organ size In contrast to apoptotic implosion, cellular necrosis can be likened to an explosion, in which cellular contents are spewed into the extracellular space; this process is often referred to as a "dirty death," as the debris provokes a robust, but less well-controlled, inflammatory response Regardless of the nature of the initiation signal that triggers apoptosis, all pathways converge on common effectors, the caspases This property underscores the "ready-to-go" nature of intrinsic defense: induction of apoptosis requires sequential activation of proteins that are already present in the cytoplasm (a rapid event), in contrast to a more time-consuming response that requires transcription and protein synthesis Two convergent caspase activation cascades are known: the extrinsic and intrinsic pathways . Apoptosis is a defense against viral infection In many infections, A series of chemical the target cell is reactions that lead A part of the nondividing and to blood clotting, or a coagulation cascade quiescent, and hence system of chemical that initiates blood unable to provide and energetic clotting when tissue is the enzymes and networks that form injured other proteins the basis for needed for emotions and reproduction of the memories infecting virus Such processes are often referred to as "altruistic"; upon detection that something is wrong within, a cell initiates a program of cell death, removing itself from the population from the greater good of the host Viral gene products that modulate apoptosis Mutant viruses unable to inhibit apoptosis were first detected because the host DHA of infected cells was unstable (a hallmark of apoptosis); the cells lysed rapidly upon infection Counterintuitively, some viruses produce proteins that promote apoptosis, perhaps to aid in virus release These membranes possess cellular markers of apoptosis, including phosphatidylserine, which normally bind to receptors that are present on the surface of phagocytic cells and that initiate endocytosis of debris Apoptosis is monitored by sentinel cells Phagocytes, like dendritic cells and macrophages, reside in areas of the body where microbes are most likely to invade, including skin and mucous membranes Phagocytes gather information by taking up cellular debris and extracellular proteins released from apoptosing cells Such cell-cell communication, the interface between the innate and adaptive arms of host immunity, informs T cells about the nature of the insult in peripheral tissues; antigen-specific T cells become activated accordingly, eventually migrating to the site of infection A core principle that this process exemplifies should now be quite familiar: a modest initial signal that occurs in a single infected cell leads to a cascade of subsequent events that vastly amplifies the host response Programmed necrosis (necroptosis) Following engagement of the TLR3, TLR4, and death receptors in the TNF receptor superfamily, necroptosis is mediated by two kinases, RIPK1 and RIPK3 (receptor interacting serine/threonine protein kinases 1 and 3) Both DAI and RIPK3 have RIP homotypic interaction motifs (RHIMs); when DAI detects nucleic acids produced by replicating MCMV and other viruses, it uses its RHIM to engage RIPK3 and activate necroptosis The viral immediate early protein 3 (IE3), a crucial transcriptional activator for this virus, was required for DAI activation, and mutation of residues in the DAI Z-DNAbinding domain abolished this response Both pathways can be triggered simultaneously; whether the infected cell dies by either process is stochastic, and perhaps cell-type specific Autophagy This process, autophagy, allows for recycling of cellular components, but is also an effective way to target incoming viruses to the lysosomal pathway Infection by many viruses induces a state of metabolic stress that normally triggers intrinsic defenses, including stress-induced alterations in translation that are modulated in part by eIF2-alpha kinases Additionally, autophagy can restrict viral replication by transfer of viral nucleic acids to endosomal compartments to stimulate innate immune responses via TLRs, or can expedite delivery of viral antigens to major histocompatibility complex class I and II molecules to facilitate antigen presentation Alternatively, viral products can trigger selective autophagy to degrade lipids as a source of energy or to subvert detection by selectively degrading sensing proteins Epigenetic silencing Epigenetic changes do not affect the nucleotide sequence, but rather add or remove modifications to the existing nucleotides or chromosomal histones that promote chromatin condensation or decondensation, making genes less or more accessible to the transcriptional machinery Acetylation removes the positive charge on the histones, thereby converting acetylated regions of chromatin into more-relaxed structures, associated with easier access to the DNA and greater opportunities for transcription Upon entering the nucleus, foreign DNA molecules can be organized quickly into transcriptionally silent chromatin, an intrinsic defense that limits viral genome expression and replication but may also allow the the virus to establish A long-term infection in the host cell Host proteins that restrict virus reproduction (restriction factors) Targeting viral genomes ZAP Host-encoded methyltransferases methylate the C residue of CpG pairs; over time, deamination converts methylated C s into T s, purging the genome of CpG pairs Interestingly, although ZAP has four zinc-finger domains, which could theoretically all engage dinucleotides, only the second zinc finger does so Deaminases APOBEC Enzymes such as the zinc-finger containing family of cytosine deaminases can also inhibit virus reproduction APOBEC —> apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like AID (activation-induced deaminase) does not act directly against viruses but is crucial for the anybody diversification process, because it results in DNA breaks that are imprecisely resolved by the cellular repair machinery, leading to somatic hypermutation Typically, APOBEC3 members reside in or shuttle to the cytoplasm, where they can bind mature viral RNAs, allowing them to be ferried into budding viral particles RNA interference When a single-stranded RNA virus infects a cell, among the first steps in its reproduction is the synthesis of a strand complementary to the incoming genome that also produces transient, double-stranded intermediates In contrast to siRNAs, miRNAs are derived from the host genome and processed from precursors that form RNA hairpins that are partially double-stranded Secreted mediators of the innate immune response Vocab Chemokines: secreted mediators that influence the migration of immune cells to sites of infection Interferons: those that activate antiviral programs Cytokines: the diverse collection of other cellfree molecules It is likely that various cytokines and interferons bind receptors on a single cell, transducing distinct, and perhaps conflicting signals Overview of cytokine functions IFN is synthesized and secreted when a cell detects a foreign nucleic acid or when TLR is engaged. In turn, locally released IFN activates a more global innate immune response, should viral reproduction continue unabated In unstimulated cells, NF-kB dimers are retained in the cytoplasm by a family of inhibitors, called IkBs (inhibitors of NF-kB), which block the nuclear localization signals on NF-kB, keeping it sequestered in an inactive state in the cytoplasm Four different mechanisms, induced by virus infection, lead to destruction of IkB, freeing NF-kB to transit to the nucleus and initiate transcription of IFN genes (1) signal transduction pathways leading to IkB destruction may be activated upon binding of a virus particle to its receptor (2) viral proteins synthesized in the infected cell can directly engage signal transduction pathways that culminate in NF-kB activation (3) cellular pattern recognition receptors, including RIG-I/MDA5 and PKR, can lead to activation of NF-kB (4) over-production of viral proteins in the endoplasmic reticulum can cause release of calcium ions, which in turn activates NF-kB Secreted IFNs engage receptors on sentinel dendritic cells, macrophages, and adjacent uninfected cells, which then synthesize a distinct set of cytokines, amplifying the initial response Pro-inflammatory cytokines stimulate the liver to synthesize acute-phase proteins, many of which are required to repair tissue damage and to clear the infection The former proteins have been called virokines if they mimic host cytokines, or viroceptors if they mimic host cytokine receptors Virokines competitively inhibit the binding of host signaling molecules to their target receptors, whereas viroceptors mimic host receptors and thus divert signaling molecules from finding their targets Interferons, cytokines of early warning and action Type I IFN synthesis While type I IFNs are induced principally following detection of infection and signaling by pattern recognition receptors and their downstream partners, other signals can also lead to IFN production The production of IFN by infected cells and uninfected, immature dendritic cells at the site of infection is rapid and robust, but transient; it occurs within hours of infection and generally declines by 8 to 12 h post-exposure IFN signaling Cells that produce IFN may also respond to IFN, but it must first be secreted, and then bind to cellular receptors. A cell without IFN receptors may synthesize IFN but cannot be affected by this cytokine IFNs affect gene expression by signaling via the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) pathway Components of this signal transduction cascade can also respond to IL-6 and other cytokines There are four known JAK kinases and seven structurally and functionally related STAT proteins IFN produces an antiviral state Shortly after infection of the host, newly made IFN released from infected cells and local immature dendritic cells can be found circulating in the body, but its concentration is highest at the site of infection, where it is bound by any cell with the appropriate receptor Cells that bind and respond to IFN fail to support the reproduction of many different viruses; they are said to be in an antiviral state IFN not only induces death of the infected cells, but also ensures that uninflected cells in the vicinity are prepared to undergo apoptosis should they become infected Some IFN-induced gene products and their antiviral actions Double-stranded RNA-activated protein kinase Establishment of the PKR-mediated antiviral state is a two-step process, in which IFN promotes the increased production and accumulation of a protein that become activated only when it encounters double-stranded viral RNA The signal transduction cascade imitated by IFN binding to its receptor leads to a dramatic increase in the concentration of inactive PKR Phosphorylated eIF2-alpha does not invariably lead to cell death, however, as this modified protein can also trigger autophagy or, when minimally activated, localized decrease in protein synthesis without cell death Ubiquitin-proteasome pathway components The protease is a large, multisubunit protease that degrades cytoplasmic and nuclear proteins targeted for proteolysis by polyubiquitinylation Chemokines Chemokines, secreted by local macrophages and some infected cells, bind to G proteincoupled receptors on circulating lymphocytes, inducing signaling pathways involved in cell movement and activation First, selectins on the endothelium interact with mucin receptors on the leukocyte, causing it to roll along the cell surface, slowing its transit, and enabling it to migrate through the blood vessel Virus-encoded chemokine homologs function as agonists, binding to cellular receptors and transducing signals; or antagonists, preventing the activity of chemokines by occupying chemokine receptors The Innate immune response When intrinsic cell defenses are unable to stop the spread of infection, the combination of cell death, local increasing concentrations of cytokines, and release of other stress-related molecules around the area of infection leads to activation of the next phase of host defense, the innate immune response In addition to these effectors, the innate response also incorporates a large collection of serum proteins called complement, and cytolytic lymphocytes called natural killer cells (NK cells) While the speed and potency of innate immunity is important, this response must also be transient, because its continued activity is damaging to the host Complement The name "complement" derived from the ability of this blood component to cooperate with antibodies and phagocytic cells to clear an infection There are three distinct pathways in the complement system: the classical pathway, alternative pathway, and lectin pathway Complement action can be initiated following direct recognition of a microbial invader by C1q (a component of C1) in the classical pathway, or by recognition of cleaved C3b proteins in the alternative pathway The complement cascade A crucial property of C3 and C5 converts enzymes is that they are bound covalently to the surface of the pathogen or the infected cell The action of surface-bound C3 convertase on its substrate yields C3b, the primary effector of all three complement pathways, and C3a, a potent, secreted mediator of inflammation Complement components released locally aid in recruitment of monocytes and neutrophils to the site of infection, stimulate their activities, and increase vascular permeability "Natural antibody" protects against infection The anti-alpha-Gal antibody-complement reaction is probably the primary reason why humans and higher primates are resistant to infection by enveloped viruses of other animals, despite the ability of many of these viruses to infect human cells in culture efficiently Natural killer cells Natural killer cells are at the front line of innate defense: they are prepared to recognize and kill some virus-infected cells, and do not need selection or stimulation to do so NK cells are stimulated to divide whenever infected cells and sentinel dendritic cells make IFN