pathways 151,153,154.
Highlighting the role of the sensing of viral DNA during immunity to retroviruses, HIV-‐1 capsid binds the cellular cyclophilin A and CPSF6 as cofactors to escape to recognition of the reverse-‐transcription products by as yet unidentified cytosolic sensors that would otherwise restrict replication in a type I IFN-‐dependent manner 155.
1.2.2 The innate immune pathways
Two important routes that PRRs use to activate the innate immune response are via the AP-‐1-‐ and the NFκB-‐ mediated signaling (figure 5). The activation of the MAPK-‐dependent pathway is initiated with the stimulation of different MAPK kinase kinases (MAP3Ks) and continues with a cascade of subsequent phosphorylations of a target MAPK kinase (MAP2K) that will in turn act on a specific MAPK 115. Three routes of the MAPK signaling pathway have been extensively studied and are involved in one or both of the pro-‐inflammatory and anti-‐inflammatory processes during the immune response: the extracellular signal-‐regulated kinase (ERK), Jun N-‐terminal Kinase (JNK) and protein of 38 kDa (p38) pathways (figure 7). The corresponding studies are mainly based on the effect of the stimulation of TLRs.
The ERK1 and ERK2 branch involves the activation, upon engagement of a TLR, of the tumor progression locus 2 (TPL2) 156. This MAP3K in turns activate MAPK kinase1 (MKK1) and MKK2. This pathway leads to the production of from one side the pro-‐inflammatory cytokines tumor TNF-‐α and interleukin 1 beta (IL-‐1β), from the other side the anti-‐inflammatory IL-‐10 115,157,158. ERK1 and ERK2 additionally have a repressive action on the expression of IL-‐12 and the two antiviral proteins IFNβ and inducible nitric oxide synthase (iNOS) 158,159.
The stimulation of the complex formed by the MAP3K TAK1 and Tab2/Tab3, results in the phosphorylation of the components of three main pathways. The
first route involves the activation if the IKK complex, leading to the enhancement of the ERK1/2-‐ and NFκB-‐ mediated pathways. The targeting of, from one side MKK4 and 7, from another side MKK3 and 6, will result in the up-‐regulation of JNK-‐ and p38-‐ stimulated genes, respectively 115.
JNK-‐mediated signaling was shown to contribute in myeloid cells to the establishment of the acute inflammatory M1 macrophage phenotype 160.
The p38 MAPK isoform alpha (p38α), for his part, has dual roles. Depending on the cell line and the type of induced-‐damage examined, p38α enhances or decreases the inflammatory response 115,161,162.
The ERK1/2 MAPKs phosphorylate the nuclear transcription factors c-‐AMP response-‐element binding protein (CREB), cMyc and cFos. The latter protein associates with one of the targets of JNK, cJun, to form one type of activator protein-‐ 1 (AP-‐1) transcription complex. Alternatively, cJun can homodimerize or associates with the ATF2 transcription factor that is phosphorylated by p38
115.
The different AP-‐1 transcription factor complexes are involved in different contrary processes such as cell proliferation and apoptosis, inflammatory potentiation and modulation 163. These opposite effects are mediated in part by differential combinations of transcription factors that will form heterodimers with different target genes. Consistently, the binding of cJun with cFos or ATF2 will result in cell growth or neuronal apoptosis, respectively 164. An alternative way to direct AP-‐1 in one or another pathway is by the expression of JNK targets that antagonize the action of cJun-‐containing complexes, as it seems to be the case for JunB, in the context of cJun-‐promoted cell growth 165,166. The AP-‐1 transcritption factors additionally activate a plethora of target genes that are involved in the innate immune response and the inflammatory process. Dimers of Jun and Fos can cooperate with the nuclear factor of activated T cells (NFAT) to activate the expression of cytokines as IL-‐2, IL-‐3, IL-‐4, IL-‐5 and IL-‐13, that of molecules playing a role in humoral immunity such as CD25, as well as that of
the inducer of inflammatory prostaglandins, cyclooxygenase 2 (COX2) 167. Additionally, AP-‐1 stimulates the expression of the type I IFN, alone or in combination with other transcription factors such as signal transducers and activators of transcription 4 (STAT4) 168-‐170. Inflammatory cytokines in turn up-‐
regulate the MAPK-‐dependent pathway 163.
As Type I IFN production induces, among other pathways, AP-‐1-‐mediated signaling and the expression of ISGs, it constitutes the second wave of innate immune activation and the MAPK-‐mediated pathway is thus an early response component. Similarly, NFκB activity is stimulated by inflammatory cytokines, including IFNβ 171-‐173, to induce successively the expression of genes involved in the innate immune response.
The NFκB family of transcription factors is composed of six members, namely p50, p52, RelA, RelB, c-‐Rel and v-‐Rel 172. Similar to the AP-‐1 family, these proteins associate in different combinations of homo-‐ or hetero-‐dimers. All the NFκB proteins are composed of an N-‐terminal Rel-‐homology domain (RHD) that allows them to bind to DNA as well as to dimerize, and a nuclear-‐localization signal (NLS) that directs them to the nucleus when free from the inhibitor.
Except for p50 and p52, the other NFκB members carry a C-‐terminal transcription activation domain (TAD) that allows them to stimulate the synthesis of gene transcripts. For this reason, p50 and p52 need to heterodimerize with other proteins as RelA or RelB to act as transactivators 174-‐
176. When found in a homodimeric form, p50 and p52 act as transcriptional repressors 173.
In most unstimulated cells, the NFκB complexes are bound to inhibitor proteins called inhibitors of κB (IκB) and reside in the cytoplasm. Upon activation of the upstream kinases IκB kinases (IKKs), IκB is phosphorylated then degraded and the NFκB transcription complex can enter the nucleus to bind particular sites in the promoter of specific genes 177.
The IKK proteins are activated via two alternative pathways, namely the canonical and non-‐canonical signaling routes 173. The conventional pathway is initiated with most of the stimuli leading to NFκB activation, such as ligand binding to a TLR and the TNFα interaction with its receptor. Upon recognition of TNFα by the TNF 1 receptor (TNF1R), the TNF1R-‐associated protein with DEATH domain (TRADD) acts as a scaffold for the recruitment of Fas-‐associated protein with DEATH domain (FADD) and TRAF2 or TRAF5 173.
The E3 ubiquitin-‐ligase activity of TRAF2 or TRAF5, similar to that of TRAF6, mediates the activation of RIP1 by K63-‐linked polyubiquitination 178. This protein modification allows RIP1 to interact with the TAK1 complex via Tab2 and Tab3, which subsequently leads to phosphorylation of the IKKβ component within the IKK complex also formed by IKKα and IKKγ (NEMO) 179,180. In this way activated, the IKK complex phosphorylates the IκB, targeting it to the proteasome and releasing the NFκB complexes to allow them to enter the nucleus and activate target genes (figure 6).
In the case of the TLR4 signaling via MyD88, the scaffold protein is TRAM and the activation of the TAK1 complex involves TRAF6 173, as seen above for the AP-‐
1 pathway. The TAK1 kinase is thus a central component of the innate immune response and mediates the convergence of different stimulated receptors as PRRs and cytokine receptors to the activation of the MAPK and NFκB pathways.
This constitutes a means of producing cytokines, antiviral proteins, and negative feed-‐back loops, all of which are important in the context of infection and in the setting and the modulation of the inflammation.
Other cytokines from the TNF family, such as CD40L and lymphotoxin-‐β (LT-‐β), activate the non-‐canonical NFκB pathway, via the phosphorylation of an IKKα dimer by the NFκB-‐inducing kinase (NIK) 181. The phosphorylated IKKα interacts with the p100 NFκB precursor and process it into p52. The dimer composed of p52 and RelB is then competent to migrate into the nucleus and regulate gene expression 181.
As reviewed by Bonizzi and Karin 172, the NFκB transcription factors up-‐regulate the expression of cytokines, chemokines, other proinflammatory and/or antiviral molecules as iNOS, COX2, as well as that of adhesion molecules, essential for cell-‐
to-‐cell contacts during the immune response. Thus, similar to AP-‐1, depending on different combinations of transcription factors, NFκB-‐mediated pathway can lead to apoptosis or survival and this property allows these proteins to play a role at different stages of development and survival of immune cells such as neutrophils, DCs, natural killer (NK) cells, T lymphocytes and B cells 173.
Figure 7: Simplified representation of the MAPK and NFKB pathways. When an E3 ligase (green hexagone) such as TRAF6 or TRIM5 synthesizes poly-‐ubquitin chains (blue circles, Ub), the TAB2/TAB3/TAK1 complex gets activated and stimulates kinases of the p38 and JNK family, resulting in the activation of different complexes of AP-‐1 transcription factors (red and green imbricated shapes). The IKK complex is also activated by TAK1 and results in the stimulation of different NFκB transcription factors (yellow and blue imbricated shapes). The activation of ERK1 and ERK2 is mediated via the stimulation of the TPL2-‐dependent pathway.
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1.2.3 Immunity to retroviruses: restriction factors
The replication ability of retroviruses in different cells depends on many cellular factors. The first considered factor is the entry of the retrovirus into the cell cytoplasm, via recognition of the corresponding receptor. For example, as discussed previously, HIV-‐1 entry requires the recognition of the CD4 receptor and a coreceptor, principally CXCR4 or CCR5. The subsequent steps of the viral life cycle exploit host proteins in a species-‐dependent way to proceed, as highlighted by the inability of HIV-‐1 to productively infect murine cell lines that have been engineered to express human CD4 182 and taking into account that the murine CXCR4 can be used as a coreceptor by HIV-‐1 183. Importantly, murine cells have a cyclin T1 protein, that HIV-‐1 Tat does not bind because of a species-‐
specific polymorphism, thus precluding the employment of this cofactor required for the transactivation of LTR-‐directed expression 184. When circumventing this post-‐entry blocks by expression of human Cyclin T1, some murine cell lines proceed into viral gene transcription, but further steps are blocked, as mRNA export and processing, as well as virion assembly 185,186. These blockades are rescued upon fusion of murine and human cells, showing that there are factors exerting a positive effect on viral replication late steps that are not present in the mouse 187.
Interestingly, in contrast to fibroblasts, murine T cells do not support HIV-‐1 reverse transcription 183. The blockade of a pre-‐integration step of the viral replication strongly recalls other phenotypes observed in mice and primates.
The cell tropism is not only dictated by the presence or the absence of positive cofactors in a cell.
The first indirect report of a negative factor influencing retroviral replication was in 1957 by C. Friend who discovered that a genetic transmissible trait