Inhibition of TLR2 signaling by small molecule inhibitors targeting a pocket within the TLR2 TIR domain

Toll-like receptor (TLR) signaling is initiated by dimerization of intracellular Toll/IL-1 receptor resistance (TIR) domains. For all TLRs except TLR3, recruitment of the adapter, myeloid differentiation primary response gene 88 (MyD88), to TLR TIR domains results in downstream signaling culminating in proinflammatory cytokine production. Therefore, blocking TLR TIR dimerization may ameliorate TLR2-mediated hyperinflammatory states. The BB loop within the TLR TIR domain is critical for mediating certain protein–protein interactions. Examination of the human TLR2 TIR domain crystal structure revealed a pocket adjacent to the highly conserved P681 and G682 BB loop residues. Using computer-aided drug design (CADD), we sought to identify a small molecule inhibitor(s) that would fit within this pocket and potentially disrupt TLR2 signaling. In silico screening identified 149 compounds and 20 US Food and Drug Administration-approved drugs based on their predicted ability to bind in the BB loop pocket. These compounds were screened in HEK293T-TLR2 transfectants for the ability to inhibit TLR2-mediated IL-8 mRNA. C₁₆H₁₅NO₄ (C29) was identified as a potential TLR2 inhibitor. C29, and its derivative, ortho-vanillin (o-vanillin), inhibited TLR2/1 and TLR2/6 signaling induced by synthetic and bacterial TLR2 agonists in human HEK-TLR2 and THP-1 cells, but only TLR2/1 signaling in murine macrophages. C29 failed to inhibit signaling induced by other TLR agonists and TNF-α. Mutagenesis of BB loop pocket residues revealed an indispensable role for TLR2/1, but not TLR2/6, signaling, suggesting divergent roles. Mice treated with o-vanillin exhibited reduced TLR2-induced inflammation. Our data provide proof of principle that targeting the BB loop pocket is an effective approach for identification of TLR2 signaling inhibitors.Toll-like receptors (TLRs) are type I transmembrane receptors that detect conserved “pathogen-associated molecular patterns” from microbes, as well as host-derived “danger-associated molecular patterns” (1). TLR2 heterodimerizes with TLR6 or TLR1 to recognize diacyl lipopeptides or triacyl lipopeptides, respectively (2, 3), present in gram-positive and gram-negative bacteria (4–9).Ligand engagement of TLR2/1 or TLR2/6 activates the myeloid differentiation primary response gene 88 (MyD88)-dependent pathway (i.e., nuclear translocation of NF-κB, activation of MAPKs), resulting in production of proinflammatory cytokines (10). Dysregulated TLR2 signaling has been implicated in numerous diseases (e.g., sepsis, atherosclerosis, tumor metastasis, ischemia/reperfusion injury) (11–14). Several inhibitors of TLR2 signaling have been developed (15–18), yet none is licensed for human use. A better understanding of the Toll/IL-1 receptor resistance (TIR) domain interactions involved in TLR2 signaling could lead to novel therapeutic agents.Both TLRs and adapter proteins contain a cytoplasmic TIR domain that mediates homotypic and heterotypic interactions during TLR signaling (19). Two adapter proteins implicated in TLR2 signaling are MyD88 and TIRAP (Mal). A conserved Pro [e.g., P681 in human TLR2 (hTLR2), P712 in murine TLR4 (mTLR4), P674 in hTLR10, P804 in mTLR11] within the BB loop of almost all TIR domains is critical for signaling (20–27). More importantly, the BB loop P681H mutation in hTLR2 abolished recruitment of MyD88 and signaling (20, 26). Based on this evidence, the BB loop within the TLR2 TIR domain appears to be an ideal target for attenuation of TLR2 signaling.Visual inspection of the crystal structure of the hTLR2 TIR domain (26) revealed a pocket formed by residues on the β-B strand and α-B helix that includes the highly conserved Pro and Gly residues of the BB loop. We hypothesized that targeting this pocket with a small molecule might inhibit interaction of TLR2 with MyD88, and thereby blunt TLR2 signaling. We identified C₁₆H₁₅NO₄ (C29) and its derivative, ortho-vanillin (o-vanillin), which inhibit mTLR2 and hTLR2 signaling initiated by synthetic and bacterial agonists without cytotoxicity. Interestingly, mutation of the BB loop pocket residues revealed a differential requirement for TLR2/1 vs. TLR2/6 signaling. Our data indicate that computer-aided drug design (CADD) is an effective approach for identifying small molecule inhibitors of TLR2 signaling and has the potential to identify inhibitors for other TLR signaling pathways.     

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling

Homotypic and heterotypic interactions between Toll/interleukin-1 receptor (TIR) domains in Toll-like receptors (TLRs) and downstream adaptors are essential to evoke innate immune responses. However, such oligomerization properties present intrinsic difficulties in structural studies of TIR domains. Here, using BB-loop mutations that disrupt homotypic interactions, we determined the structures of the monomeric TIR domain-containing adaptor molecule (TICAM)-1 and TICAM-2 TIR domains. Docking of the monomeric structures, together with yeast two hybrid-based mutagenesis assays, reveals that the homotypic interaction between TICAM-2 TIR is indispensable to present a scaffold for recruiting the monomeric moiety of the TICAM-1 TIR dimer. This result proposes a unique idea that oligomerization of upstream TIR domains is crucial for binding of downstream TIR domains. Furthermore, the bivalent nature of each TIR domain dimer can generate a large signaling complex under the activated TLRs, which would recruit downstream signaling molecules efficiently. This model is consistent with previous reports that BB-loop mutants completely abrogate downstream signaling.The extracellular domain of toll-like receptor 4 (TLR4) specifically binds lipopolysaccharides (LPSs) from Gram-negative bacteria, inducing dimerization and leading to the dimerization of cytosolic Toll/interleukin-1 receptor (TIR) domains. This activated conformation of TLR4 recruits the TIR domain of a downstream adaptor molecule, TIR domain-containing adaptor molecule-2 (TICAM-2) [also known as TRIF-related adaptor molecule (TRAM)], that subsequently recruits the TIR domain of another adaptor molecule, TIR domain-containing adaptor molecule-1 (TICAM-1) [also known as TIR domain-containing adaptor inducing IFN-β (TRIF)] (1–3) at endosomes. Eventually this process activates IFN response factors and generates type-I interferons (IFNs) (4–7). Elucidation of the homotypic and heterotypic interactions between TICAM-1 and TICAM-2 is essential for understanding of TLR4-mediated type-I IFN generation (8).A large number of TIR domain structures, including receptors and adaptors, have been determined by X-ray crystallography and NMR. The receptors include TLR1 (9), TLR2 (10), and IL-1R accessory protein-like (IL-1RAPL) (11). Adaptors include myeloid differentiation factor 88 (MyD88) (12) and MyD88 adaptor-like (Mal) (13, 14). In addition, AtTIR (15, 16) derived from Arabidopsis thaliana and PdTIR (17) from bacteria have been solved. Each of these TIR domain structures has a ferredoxin fold with five β-strands (βA–βE), five α-helices (αA–αE), and loops connecting β-strands and α-helices (9). Although homotypic interactions of the TIR domains have been proposed based on the crystal structures, most proposed models have small interacting surfaces, possibly due to crystal contacts. Recently, however, a crystal structure of the TLR10 TIR domain was reported that forms a homotypic dimer mediated by the loop connecting βB and αB (designated “BB-loop”) (18). Interestingly, BB-loop mutations in TLR4 were reported to be dominant-negative and abrogated downstream signaling (19). TICAM-1 and TICAM-2 harboring BB-loop mutations are also dominant-negative and unable to form homotypic interactions (1, 2), reinforcing the importance of BB-loop–mediated homotypic dimer formation in signal propagation.Despite extensive structural studies, it is not known why homotypic interactions are essential for downstream signaling (20–27). To address this issue, it is necessary to discriminate residues required for homotypic and those required for heterotypic interactions. Here, we first determine the structures of the monomeric BB-loop mutants of the TICAM-1 and TICAM-2 TIR domains using NMR. Then, based on the solution structures of the BB-loop mutants, coupled mutagenesis/yeast two-hybrid experiments, and restrained docking calculations, we show that the homotypic interaction of TICAM-2 TIR is essential to form a scaffold for recruiting the TICAM-1 TIR domain.     

CD14 dependence of TLR4 endocytosis and TRIF signaling displays ligand specificity and is dissociable in endotoxin tolerance

Dimerization of Toll-like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD2) heterodimers is critical for both MyD88- and TIR-domain–containing adapter-inducing IFN-β (TRIF)-mediated signaling pathways. Recently, Zanoni et al. [(2011) Cell 147(4):868–880] reported that cluster of differentiation 14 (CD14) is required for LPS-/Escherichia coli- induced TLR4 internalization into endosomes and activation of TRIF-mediated signaling in macrophages. We confirmed their findings with LPS but report here that CD14 is not required for receptor endocytosis and downstream signaling mediated by TLR4/MD2 agonistic antibody (UT12) and synthetic small-molecule TLR4 ligands (1Z105) in murine macrophages. CD14 deficiency completely ablated the LPS-induced TBK1/IRF3 signaling axis that mediates production of IFN-β in murine macrophages without affecting MyD88-mediated signaling, including NF-κB, MAPK activation, and TNF-α and IL-6 production. However, neither the MyD88- nor TRIF-signaling pathways and their associated cytokine profiles were altered in the absence of CD14 in UT12- or 1Z105-treated murine macrophages. Eritoran (E5564), a lipid A antagonist that binds the MD2 “pocket,” completely blocked LPS- and 1Z105-driven, but not UT12-induced, TLR4 dimerization and endocytosis. Furthermore, TLR4 endocytosis is induced in macrophages tolerized by exposure to either LPS or UT12 and is independent of CD14. These data indicate that TLR4 receptor endocytosis and the TRIF-signaling pathway are dissociable and that TLR4 internalization in macrophages can be induced by UT12, 1Z105, and during endotoxin tolerance in the absence of CD14.Toll-like receptor 4 (TLR4) signaling plays a crucial role in host defense against Gram-negative bacteria by recognizing the outer membrane component, lipopolysaccharide (LPS) (1–3). TLR4 signaling is initiated by transfer of an LPS monomer from LPS binding protein (LBP) to cluster of differentiation 14 (CD14) (GPI-linked or soluble). In turn, CD14 transfers monomeric LPS to myeloid differentiation factor 2 (MD-2), a protein that associates noncovalently with TLR4 (4). Appropriate ligand binding to MD2 results in dimerization of two TLR4/MD2 complexes (4). TLR4 is unique in that it is the only TLR that activates both myeloid differentiation primary response 88 (MyD88) and TIR-domain–containing adapter-inducing IFN-β (TRIF)-dependent signaling pathways (5, 6). MyD88-mediated, TLR4 signaling occurs mainly at plasma membranes and involves IL-1R–associated kinases phosphorylation, association of TNF-receptor–associated factor 6, and downstream signaling that results in NF-κB activation and induction of proinflammatory mediators such as TNF-α and IL-6 (7). In contrast, TRIF-mediated signaling in response to LPS occurs at the endosomal membrane after internalization of the TLR4 that, in turn, activates IFN regulatory factor 3 (IRF3), resulting in production of IFN-β, IP-10, and other IRF-3–dependent genes, as well as delayed NF-κB activation (8). Recent studies have shown that the endocytosis of TLR4 is tightly controlled by several molecules. Rab11a, ARF6, and p120-catenin have been implicated in Escherichia coli/LPS-induced TLR4 endocytosis and IRF3 activation (9–11). Zanoni et al. showed that CD14 plays critical roles in translocation of TLR4 into endosomes and in activation of IRF3 that are dependent upon the enzymatic activities of PLCγ2 and Syk (12). However, CD14-independent TLR4 endocytosis and TRIF signaling have not been reported.UT12 is a monoclonal antibody (MAb) with specificity for the mouse TLR4/MD2 complex and mediates LPS-like signaling (13). It has been shown that UT12 induces endotoxic shock-like symptoms in mice including augmentation of TNF-α and IL-6. Furthermore, UT12 induced long-term tolerance and protection against LPS-induced lethal shock in mice (14). However, the ability of UT12 to induce translocation of TLR4/MD2 into endosomes, as well as its potential for mediating TRIF-dependent signaling, has not been reported. Recently, a group of substituted pyrimido[5,4-b]indoles, synthetic ligands for TLR4 that activate NF-κB that act in a CD14-independent manner, were discovered by high-throughput screening (15). These synthetic ligands induced IL-6 and IP-10 in a TLR4/MD2-dependent, but CD14-independent manner (16). They, too, have not been tested for TLR4 endocytosis and TRIF-dependent intermediates.In this study, we report, for the first time to our knowledge, CD14-independent translocation of TLR4 to endosomes and TRIF signaling by UT12 and small synthetic TLR4 ligands (1Z105). A TLR4 antagonist, Eritoran, that binds to a deep hydrophobic pocket in MD2 and blocks signaling induced by LPS, UT12, and 1Z105, blocked only TLR4 internalization and dimerization induced by LPS and 1Z105. Despite TLR4/MD2 internalization, endotoxin-tolerized macrophages fail to activate TRIF-mediated signaling. These findings reveal previously unidentified insights into the possible role of CD14 in LPS-mediated TLR4 endocytosis and signaling and demonstrate that TLR4 endocytosis and signaling are dissociable processes.     

TLR8 on dendritic cells and TLR9 on B cells restrain TLR7-mediated spontaneous autoimmunity in C57BL/6 mice

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with diverse clinical presentations characterized by the presence of autoantibodies to nuclear components. Toll-like receptor (TLR)7, TLR8, and TLR9 sense microbial or endogenous nucleic acids and are implicated in the development of SLE. In mice TLR7-deficiency ameliorates SLE, but TLR8- or TLR9-deficiency exacerbates the disease because of increased TLR7 response. Thus, both TLR8 and TLR9 control TLR7 function, but whether TLR8 and TLR9 act in parallel or in series in the same or different cell types in controlling TLR7-mediated lupus remains unknown. Here, we reveal that double TLR8/9-deficient (TLR8/9^−/−) mice on the C57BL/6 background showed increased abnormalities characteristic of SLE, including splenomegaly, autoantibody production, frequencies of marginal zone and B1 B cells, and renal pathology compared with single TLR8^−/− or TLR9^−/− mice. On the cellular level, TLR8^−/− and TLR8/9^−/− dendritic cells were hyperesponsive to TLR7 ligand R848, but TLR9^−/− cells responded normally. Moreover, B cells from TLR9^−/− and TLR8/9^−/− mice were hyperesponsive to R848, but TLR8^−/− B cells were not. These results reveal that TLR8 and TLR9 have an additive effect on controlling TLR7 function and TLR7-mediated lupus; however, they act on different cell types. TLR8 controls TLR7 function on dendritic cells, and TLR9 restrains TLR7 response on B cells.Systemic lupus erythematosus (SLE) is a complex chronic autoimmune disease that arises spontaneously and is characterized by production of autoantibodies against self-nucleic acids and associated proteins (1). These autoantibodies bind self-nucleic acids released by dying cells and form immune complexes that accumulate in different parts of the body, leading to inflammation and tissue damage. The kidneys, skin, joints, lungs, serous membranes, as well as, the cardiovascular, nervous and musculoskeletal system become targets of inflammation at onset or during the course of the disease (2). The etiology of SLE is unknown, yet genetics, sex, infectious agents, environmental factors, and certain medications may play a role in the initiation of the disease by causing alterations in lymphoid signaling, antigen presentation, apoptosis, and clearance of immune complexes (3, 4).Toll-like receptors (TLRs) detect specific microbial components widely expressed by bacteria, fungi, protozoa, and viruses, and initiate signaling pathways critical for induction of immune responses to infection (5). In contrast to the cell surface TLRs that detect bacterial cell wall components and viral particles, nucleic acid-sensing TLRs are localized mainly within endosomal compartments (6). Human endosomal TLRs consist of TLR3, which senses viral double-stranded RNA (dsRNA) (7), TLR7 and TLR8, which recognize viral single-stranded RNA (8–10), and TLR9, which detects bacterial and viral unmethylated CpG-containing DNA motifs (11). Interestingly, these endosomal TLRs are also able to detect self-nucleic acids (12–14). Although the endosomal localization isolate TLR3, TLR7, TLR8, and TLR9 away from self-nucleic acids in the extracellular space, still self-RNA or -DNA can become a potent trigger of cell activation when transported into TLR-containing endosomes, and such recognition can result in sterile inflammation and autoimmunity, including SLE (4, 15, 16). The connection of the endosomal TLRs with SLE originates mainly from mouse models, where TLR7 signaling seems to play a central role. TLR7 gene duplication is the cause for the development of lupus in mice bearing the Y chromosome-linked autoimmune accelerating (Yaa) locus that harbors 17 genes, including TLR7 (17, 18). In TLR7 transgenic mouse lines, a modest increase in TLR7 expression promotes autoreactive lymphocytes with RNA specificities and myeloid cell proliferation, but a substantial increase in TLR7 expression causes fatal acute inflammatory pathology and profound dendritic cell (DC) dysregulation (17). In addition, studies in several lupus-prone mouse strains have revealed that TLR7-deficiency ameliorates disease, but TLR9-deficiency exacerbates it. Interestingly, this controversy can be explained by the enhanced TLR7 activity in the TLR9-deficient lupus mice (19, 20). Although murine TLR8 does not seem so far to be able to sense a ligand (21, 22), we have shown previously that it plays an important biological role in controlling TLR7-mediated lupus. Indeed, TLR8-deficiency in mice (on the C57BL/6 background that is not prone to lupus) leads to lupus development because of increased TLR7 expression and signaling in DCs (23). Thus, tight control and regulation of TLR7 is pivotal for avoiding SLE and inflammatory pathology in mice. Recent studies in humans have also revealed that increased expression of TLR7 is associated with increased risk for SLE (24–26).Nucleic acid TLRs are expressed in many cell types, including DCs, plasmacytoid DCs (pDCs) and B cells, all of which play a central role in SLE development. TLR7, TLR8, and TLR9 signal through the adaptor molecule myeloid differentiation primary response gene 88 (MyD88), whereas TLR3 signals via the adaptor TRIF (Toll/IL-1 receptor domain-containing adaptor inducing IFN-β) (5). MyD88-deficiency abrogates most attributes of lupus in several lupus-prone mouse strains (19, 27–29). Moreover, deficiency for Unc93B1, a multipass transmembrane protein that controls trafficking of TLRs from the endoplasmic reticulum to endolysosomes and is required for nucleic acid-sensing TLR function (30), also abrogates many clinical parameters of disease in mouse lupus strains, suggesting that endosomal TLRs are critical in this disease (31). Interestingly, TLR9 competes with TLR7 for Unc93B1-dependent trafficking and predominates over TLR7 (32). TLR9 predominance is reversed to TLR7 by a D34A mutation in Unc93B1 and mice that carry this mutation show TLR7-dependent, systemic lethal inflammation (32).Thus, in mice both TLR8 and TLR9 control TLR7-mediated lupus, but it is unknown if these TLRs act in parallel or in series in the same or different cell types and if they have an additive effect or not in controlling TLR7. To address these issues, we generated double TLR8/TLR9-deficient (TLR8/9^−/−) mice and analyzed and compared the lupus phenotype in TLR8^−/−, TLR9^−/−, and TLR8/9^−/− mice. Our data revealed that TLR8/9^−/− mice have increased abnormalities characteristic of SLE and that both TLR8 and TLR9 keep TLR7-mediated lupus under control, but they act in different cell types. On DCs TLR7 function is ruled by TLR8, whereas on B cells TLR7 is mastered by TLR9.     

Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3)

Toll-like receptors (TLRs) are crucial in innate recognition of invading micro-organisms and their subsequent clearance. Bacteria are not passive bystanders and have evolved complex evasion mechanisms. Staphylococcus aureus secretes a potent TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3), which prevents receptor stimulation by pathogen-associated lipopeptides. Here, we present crystal structures of SSL3 and its complex with TLR2. The structure reveals that formation of the specific inhibitory complex is predominantly mediated by hydrophobic contacts between SSL3 and TLR2 and does not involve interaction of TLR2–glycans with the conserved Lewis^X binding site of SSL3. In the complex, SSL3 partially covers the entrance to the lipopeptide binding pocket in TLR2, reducing its size by ∼50%. We show that this is sufficient to inhibit binding of agonist Pam₂CSK₄ effectively, yet allows SSL3 to bind to an already formed TLR2–Pam₂CSK₄ complex. The binding site of SSL3 overlaps those of TLR2 dimerization partners TLR1 and TLR6 extensively. Combined, our data reveal a robust dual mechanism in which SSL3 interferes with TLR2 activation at two stages: by binding to TLR2, it blocks ligand binding and thus inhibits activation. Second, by interacting with an already formed TLR2–lipopeptide complex, it prevents TLR heterodimerization and downstream signaling.In recent years, Staphylococcus aureus has become a major health threat to both humans and domestic animals. It is found as a commensal bacterium in ∼30% of the human population, but when it becomes infectious it can cause a wide diversity of diseases, ranging from mild skin infections to life-threatening invasive conditions such as pneumonia and sepsis (1). Increased antibiotic resistance and a high amount of virulence factors secreted by S. aureus contribute to its emergence as a pathogen. Among these secreted virulence factors are the staphylococcal superantigen-like proteins (SSLs), a family of 14 proteins located on two genomic clusters (2–4). Recently, we and others identified SSL3 as a potent inhibitor of Toll-like receptor 2 (TLR2) (5, 6), an innate immunity receptor that is a dominant factor in immune recognition of S. aureus (7–10).TLR2 belongs to a family of 10 homologous innate immunity receptors that are activated by pathogen-associated molecular patterns (PAMPs) (11). TLR2 binds bacterial lipopeptides and lipoproteins. Subsequent formation of heterodimers with TLR1 or TLR6 leads to MyD88-dependent activation of the NF-κB pathway (12). TLR2 has dual ligand specificity that is determined by its dimerization partner; stimulation by diacyl lipopeptides from Gram-positive bacteria, including S. aureus, induces the formation of heterodimers with TLR6 (13), whereas triacyl lipopeptides from Gram-negative bacteria initiate formation of TLR2–TLR1 dimers (14). The structural basis for lipopeptide specificity was revealed by crystal structures of TLR2–TLR1 and TLR2–TLR6 complexes with their respective lipopeptide analogs Pam₃CSK₄ and Pam₂CSK₄: TLR2 binds two lipid tails in a large hydrophobic pocket, whereas the third lipid tail of triacyl lipopeptides is accommodated by a smaller pocket present in TLR1, but not in TLR6 (15, 16).The family of SSL proteins, including SSL3, share structural similarities to superantigens, but lack superantigenic activity. Interestingly, the functions that have been discovered for SSLs so far have all been linked to immune evasion. SSL5 inhibits neutrophil extravasation (17, 18) and phagocyte function (19, 20), SSL7 binds IgA and inhibits complement (21), and SSL10 inhibits IgG1-mediated phagocytosis (22, 23), blood coagulation (24), and the chemokine receptor CXCR4 (25). In addition to SSL3, also weak TLR2 inhibitory activity was observed for SSL4 (5), but it remains unknown whether that is its dominant function. This variety of immunomodulatory molecules and functions reflects the importance of the different components of our innate immune system in the defense against S. aureus (26).In this study we determined the crystal structures of SSL3 and the SSL3–TLR2 complex. In combination with mutagenesis and binding studies, our data provide a novel working mechanism of a functional TLR2 antagonist.     

Autoinhibition and relief mechanism by the proteolytic processing of Toll-like receptor 8

Toll-like receptor 8 (TLR8) senses single-stranded RNA (ssRNA) and initiates innate immune responses. TLR8 requires proteolytic cleavage at the loop region (Z-loop) between leucine-rich repeat (LRR) 14 and LRR15 for its activation. However, the molecular basis of Z-loop processing remains unknown. To elucidate the mechanism of Z-loop processing, we performed biochemical and structural studies of how the Z-loop affects the function of TLR8. TLR8 with the uncleaved Z-loop is unable to form a dimer, which is essential for activation, irrespective of the presence of agonistic ligands. Crystallographic analysis revealed that the uncleaved Z-loop located on the ascending lateral face prevents the approach of the dimerization partner by steric hindrance. This autoinhibition mechanism of dimerization by the Z-loop might be occurring in the proteins of the same subfamily, TLR7 and TLR9.Toll-like receptors (TLRs) constitute a family of innate immune receptors that recognize pathogen-associated molecular patterns (1). The TLR molecule is a type I transmembrane protein characterized by an extracellular leucine-rich repeat (LRR) domain, a transmembrane helix, and an intracellular Toll/interleukin-1 receptor (TIR) homology domain (2). The typical TLR molecule is considered to be monomeric in the absence of ligands, transforming into an activated dimer form on ligand binding, which allows for dimerization of the intracellular TIR domain and subsequent signaling (2).The TLR subfamily comprising TLR7, TLR8, and TLR9 recognizes single-stranded (ss) nucleic acids from viruses and bacteria (3). Specifically, TLR7 and TLR8 recognize uridine- and guanosine-rich single-stranded RNA (ssRNA) (4–11), whereas TLR9 recognizes ssDNA containing the unmethylated cytosine-phosphate-guanine (CpG) dideoxynucleotide motif (12). Furthermore, TLR7 and TLR8 are also activated by synthetic chemical compounds (13, 14), such as imiquimod (TLR7-specific), resiquimod (R848; both TLR7 and TLR8), and CL075 (both TLR7 and TLR8).Certain regulation mechanisms of the functions of the TLR7–9 subfamily members are shared because of a high degree of sequence similarities (3). They reside on the endosomal membrane, and their transportation from endoplasmic reticulum (ER) to endolysosomes is mediated by the ER membrane protein Unc93B1 (15). Moreover, TLR7–9 possess a long inserted loop region (Z-loop), consisting of ∼30 amino acid residues, between LRR14 and LRR15, and the processing by proteolytic cleavage at the Z-loop is believed to be indispensable for their function (16–21). Specifically, the processing at the Z-loop of human TLR8 mediated by furin-like proprotein convertase and cathepsins produces functional TLR8 capable of ligand binding and signaling in endolysosomes. In addition, the cleaved form of TLR8 has been found to be predominant in immune cells (16). Recent structural studies demonstrate that the N- and C-terminal halves of TLR8 after Z-loop cleavage associate with each other, and that both fragments are cooperatively involved in ligand binding (22). Moreover, a recent study revealed that the latter half of the cleaved Z-loop interacts with LRRs to stabilize the TLR8 structure and contributes to ssRNA recognition by TLR8 (23).Although accumulating evidence illustrates the functional importance of Z-loop processing at the cellular level, mechanistic insights into this processing in the regulation of TLR8 function at the molecular level are lacking. Here, to unveil the mechanistic role of Z-loop processing of TLR8, we present the results of a combined structural and biochemical investigation of TLR8 with the uncleaved Z-loop.     

Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2

Lipopolysaccharide (LPS), also known as endotoxin, activates the innate immune response through toll-like receptor 4 (TLR4) and its coreceptor, MD-2. MD-2 has a unique hydrophobic cavity that directly binds to lipid A, the active center of LPS. Tetraacylated lipid IVa, a synthetic lipid A precursor, acts as a weak agonist to mouse TLR4/MD-2, but as an antagonist to human TLR4/MD-2. However, it remains unclear as to how LPS and lipid IVa show agonistic or antagonistic activities in a species-specific manner. The present study reports the crystal structures of mouse TLR4/MD-2/LPS and TLR4/MD-2/lipid IVa complexes at 2.5 and 2.7 Å resolutions, respectively. Mouse TLR4/MD-2/LPS exhibited an agonistic “m”-shaped 2:2:2 complex similar to the human TLR4/MD-2/LPS complex. Mouse TLR4/MD-2/lipid IVa complex also showed an agonistic structural feature, exhibiting architecture similar to the 2:2:2 complex. Remarkably, lipid IVa in the mouse TLR4/MD-2 complex occupied nearly the same space as LPS, although lipid IVa lacked the two acyl chains. Human MD-2 binds lipid IVa in an antagonistic manner completely differently from the way mouse MD-2 does. Together, the results provide structural evidence of the agonistic property of lipid IVa on mouse TLR4/MD-2 and deepen understanding of the ligand binding and dimerization mechanism by the structurally diverse LPS variants.Toll-like receptors (TLRs) recognize and respond to diverse pathogenic components of microorganisms and provide the first line of defense against microbial infection (1, 2). Among the microbial components, endotoxic lipopolysaccharide (LPS) from a membrane component of Gram-negative bacteria elicits the potent innate immune response through the receptor complex of TLR4 and MD-2 (3, 4). Excessive exposure to LPS often causes exaggerated signaling via TLR4 and fatal septic shock (5, 6), which is associated with a high mortality (20–30%) and is the most common cause of death in intensive care units (5, 6).The lipid A moiety of LPS, which anchors LPS to the outer membrane of Gram-negative bacteria, is responsible for the immunostimulatory activity of LPS (7, 8). Lipid A consists of a 1,4′-bis-phosphorylated diglucosamine backbone to which variable lengths and numbers of acyl chains are covalently linked (8). The two phosphate groups are also important for the agonistic activity of lipid A because deletion of either phosphate group reduces the endotoxic activity (9, 10).TLR4 is a type I transmembrane protein composed of 22 extracellular leucine-rich repeats (LRRs), a transmembrane domain, and the Toll/IL-1 receptor domain (TIR domain) that is essential for TLR signaling and conserved among members of the Toll receptor family (1). TLR4 alone does not directly bind LPS and requires the coreceptor MD-2 (11). MD-2 is associated with the extracellular domain of TLR4 and is indispensable for LPS recognition (4). A member of the MD-2–related lipid-recognition protein family (12), MD-2 directly binds to LPS in its hydrophobic cavity with high affinity (13).Recently, the crystal structure of human TLR4/MD-2/Ra-LPS (Ra chemotype of Escherichia coli LPS) complex (14) was solved, which revealed that five of the six acyl chains of LPS are buried inside the MD-2 cavity. The sixth acyl chain lies on the surface of MD-2, partially exposed to the solvent. Together with the hydrophobic residues of MD-2, the partially exposed acyl chain constitutes the secondary binding site for the hydrophobic patch on the C-terminal convex face of the horseshoe structure of TLR4, leading to the formation of the “m”-shaped 2:2:2 hTLR4/MD-2/LPS complex. The close proximity of the C terminus of the extracellular domain in the complex induced by binding to LPS may allow for dimerization and signaling by the intracellular TIR domains (15, 16).The number and length of the acyl chains determine the agonistic property of lipid A (17–19). E. coli lipid A is usually hexaacylated and acts as a potent agonist for all mammalian cells. In contrast, tetraacylated lipid IVa, the precursor of E. coli LPS, acts as an agonist only for some mammalian species. In particular, it acts as a weak agonist on mouse and as an antagonist on human cells (20, 21). Although several studies have investigated the species-specific activity of lipid IVa (22–28), these studies primarily used mutational and computational simulation methods. Structural information on the agonistic form of TLR4/MD-2 is limited to the hTLR4/MD-2/LPS complex; no structures of mTLR4/MD-2 complexed with LPS or lipid IVa are currently available. Structural knowledge may provide critical clues regarding the agonistic and antagonistic mechanisms by LPS and lipid IVa ligands that underlie species specificity.Here, we present the two agonistic structures of mouse TLR4/MD-2/Re-LPS (Re chemotype of E. coli LPS) and TLR4/MD-2/lipid IVa complexes at 2.5 and 2.7 Å resolutions, respectively. This structural study will provide better understanding of the LPS recognition and signaling mechanism and will contribute to the development of therapeutic antiseptic shock drugs targeting TLR4/MD-2.     

TLR-dependent phagosome tubulation in dendritic cells promotes phagosome cross-talk to optimize MHC-II antigen presentation

Dendritic cells (DCs) phagocytose large particles like bacteria at sites of infection and progressively degrade them within maturing phagosomes. Phagosomes in DCs are also signaling platforms for pattern recognition receptors, such as Toll-like receptors (TLRs), and sites for assembly of cargo-derived peptides with major histocompatibility complex class II (MHC-II) molecules. Although TLR signaling from phagosomes stimulates presentation of phagocytosed antigens, the mechanisms underlying this enhancement and the cell surface delivery of MHC-II–peptide complexes from phagosomes are not known. We show that in DCs, maturing phagosomes extend numerous long tubules several hours after phagocytosis. Tubule formation requires an intact microtubule and actin cytoskeleton and MyD88-dependent phagosomal TLR signaling, but not phagolysosome formation or extensive proteolysis. In contrast to the tubules that emerge from endolysosomes after uptake of soluble ligands and TLR stimulation, the late-onset phagosomal tubules are not essential for delivery of phagosome-derived MHC-II–peptide complexes to the plasma membrane. Rather, tubulation promotes MHC-II presentation by enabling maximal cargo transfer among phagosomes that bear a TLR signature. Our data show that phagosomal tubules in DCs are functionally distinct from those that emerge from lysosomes and are unique adaptations of the phagocytic machinery that facilitate cargo exchange and antigen presentation among TLR-signaling phagosomes.Professional phagocytes take up large particles, such as bacteria, by phagocytosis and submit them to an increasingly harsh environment during phagosome maturation (1). Phagocytes concomitantly alert the immune system that an invader is present via signaling programs initiated by pattern recognition receptors, such as Toll-like receptors (TLRs) (2). Conventional dendritic cells (DCs) also alter and optimize phagosome maturation and TLR-signaling programs to preserve bacterial antigens for loading onto MHC class I and class II (MHC-II) molecules and optimize cytokine secretion to stimulate and direct T-cell responses to the invading agent (3, 4). DC presentation of soluble antigen is facilitated by TLR-driven tubulation of lysosomes that harbor MHC-II–peptide complexes and by consequent fusion of tubulovesicular structures with the plasma membrane (5–7); however, little is known about the mechanism by which signaling pathways influence the formation or presentation of phagosome-derived MHC-II–peptide complexes, key processes in the adaptive immunity to bacterial pathogens.TLRs respond to microbial ligands at the plasma membrane and in intracellular stores (8). TLR stimulation at the plasma membrane, endosomes, or phagosomes elicits distinct signaling pathways via two sets of adaptors, TIRAP (or MAL)-MyD88 and TRAM-TRIF (8, 9), which induce proinflammatory cytokine secretion and other downstream responses. TLRs such as TLR2 and TLR4 are recruited to macrophage and DC phagosomes at least partly from an intracellular pool (10–13), and signal autonomously from phagosomes independent of plasma membrane TLRs (11, 14, 15). Autonomous phagosomal signaling from TLRs or Fcγ receptors enhances the degradation of phagocytosed proteins and assembly of MHC-II with their derived peptides (14–16). Phagosomal TLR signaling has been proposed to also promote the reorganization of phagosome-derived MHC-II-enriched compartments (MIICs) to favor the delivery of MHC-II–peptide complexes to the plasma membrane (17), analogous to TLR-stimulated formation of tubules from MIICs/lysosomes (18–20) that fuse with the plasma membrane (7) and extend toward the immunologic synapse with T cells (5). Tubules emerge from phagosomes in macrophages shortly after phagocytosis and likely function in membrane recycling during early phagosome maturation stages (21–23), but tubules at later stages that might facilitate the presentation of phagosome-derived MHC-II–peptide complexes have not been reported previously. Moreover, a role for TLR signaling in formation of phagosome-derived tubules has not been established.Herein we show that in DCs, maturing phagosomes undergo extensive tubulation up to several hours after phagocytosis, and that tubulation requires TLR and MyD88 signaling and an intact actin and microtubule cytoskeleton. Unlike lysosome tubulation, phagosome tubulation is not essential for MHC-II–peptide transport to the cell surface. Rather, it contributes to content exchange among phagosomes that carry a TLR signature, and thereby enhances presentation of phagocytosed antigens from potential pathogens.     

Multifaceted contribution of the TLR4-activated IRF5 transcription factor in systemic sclerosis

Systemic sclerosis (SSc) is a multisystem autoimmune disorder with clinical manifestations resulting from tissue fibrosis and extensive vasculopathy. A potential disease susceptibility gene for SSc is IFN regulatory factor 5 (IRF5), whose SNP is associated with milder clinical manifestations; however, the underlying mechanisms of this association remain elusive. In this study we examined IRF5-deficient (Irf5^−/−) mice in the bleomycin-treated SSc murine model. We show that dermal and pulmonary fibrosis induced by bleomycin is attenuated in Irf5^−/− mice. Interestingly, we find that multiple SSc-associated events, such as fibroblast activation, inflammatory cell infiltration, endothelial-to-mesenchymal transition, vascular destabilization, Th2/Th17 skewed immune polarization, and B-cell activation, are suppressed in these mice. We further provide evidence that IRF5, activated by Toll-like receptor 4 (TLR4), binds to the promoters of various key genes involved in SSc disease pathology. These observations are congruent with the high level of expression of IRF5, TLR4, and potential endogenous TLR4 ligands in SSc skin lesions. Our study sheds light on the TLR4-IRF5 pathway in the pathology of SSc with clinical implications of targeting the IRF5 pathways in the suppression of disease development.Systemic sclerosis (SSc) is a multisystem connective tissue disease characterized by immune abnormalities, vasculopathy, and extensive tissue fibrosis (1). Based on the results of etiological and genetic studies, the conventional wisdom is that SSc is caused by a complex interplay between genetic factors and environmental influences. For instance, the biggest risk factor for SSc is family history (2). On the other hand, concordance for SSc is around 5% in twins and is similar in monozygotic and dizygotic twins, whereas antinuclear antibodies are detected more frequently in the healthy monozygotic twin sibling than in the healthy dizygotic twin sibling of an SSc patient (3). In addition, most SSc susceptibility genes are HLA haplotypes and non-HLA immune-related genes that are shared by other collagen diseases (4). Therefore, genetic factors are likely associated with autoimmunity, increasing the susceptibility to autoimmune diseases including SSc, but additional environmental factors are required to induce clinically definite SSc in genetically predisposed individuals. Despite these etiological and genetic data, the entire process of the SSc development and pathogenesis remains elusive.Therefore it is important to elucidate the molecular mechanism(s) underlying SSc pathogenesis. In this regard, much attention has been focused recently on the innate immune signaling via Toll-like receptors (TLRs) in various pathological conditions. For instance, fibroblasts and endothelial cells in SSc lesional skin highly express TLR4, originally identified as the receptor for bacterial LPS, and TLR4 signaling amplifies the sensitivity to TGF-β in dermal fibroblasts (5–7). It also was shown that dermal and lung fibrosis is attenuated in bleomycin (BLM)-treated TLR4-deficient mice (7). Endogenous potential TLR4 ligands are up-regulated in SSc lesional skin (5–7), and serum levels correlate with severe organ involvement and immunological abnormalities (8, 9). Therefore, the TLR4 signaling pathway is suspected to play a central role in the SSc pathogenesis.Although how the TLR4 signaling pathway contributes to SSc pathogenesis remains enigmatic, it is interesting that several independent case-control and genome-wide association studies identify IFN regulatory factor 5 (IRF5), a member of the IFN regulatory factor (IRF) family, as an SSc susceptibility gene (10–15). IRFs were identified primarily in the research of the type I IFN system and have been shown to have functionally diverse roles in the regulation of the innate and adaptive immune responses (16). Reflecting such property of IRFs, SNPs of IRFs have been linked to the development of various immune and inflammatory disorders. IRF5 is of particular interest, being implicated in multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and SSc (14). Thus far an association of certain SNPs within the IRF5 promoter with the risk and severity of SSc has been reported (10–15), but whether and how IRF5 is activated to contribute to disease development remains unknown.Stimulation of TLRs triggers the activation of myeloid differentiation factor 88 (MyD88)-dependent and/or independent pathways (16). IRF5 is activated via the MyD88 pathway in dendritic cells and macrophages (17). TLR-activated IRF5 mediates the induction of genes IL-6, IL-12, and TNF-α (17). Hence, an intriguing possibility is that TLR4-mediated activation of IRF5 is involved in SSc. We therefore studied the role of IRF5 in the regulation of genes associated with the susceptibility to and the severity of SSc using IRF5-deficient mice in the context of TLR4 signaling. We show that IRF5, activated by TLR4, binds to the promoters of various key genes involved in the disease symptoms. We discuss our findings in terms of the complexity of SSc and its clinical implications.     

TLR4-activated microglia require IFN-γ to induce severe neuronal dysfunction and death in situ

Microglia (tissue-resident macrophages) represent the main cell type of the innate immune system in the CNS; however, the mechanisms that control the activation of microglia are widely unknown. We systematically explored microglial activation and functional microglia–neuron interactions in organotypic hippocampal slice cultures, i.e., postnatal cortical tissue that lacks adaptive immunity. We applied electrophysiological recordings of local field potential and extracellular K⁺ concentration, immunohistochemistry, design-based stereology, morphometry, Sholl analysis, and biochemical analyses. We show that chronic activation with either bacterial lipopolysaccharide through Toll-like receptor 4 (TLR4) or leukocyte cytokine IFN-γ induces reactive phenotypes in microglia associated with morphological changes, population expansion, CD11b and CD68 up-regulation, and proinflammatory cytokine (IL-1β, TNF-α, IL-6) and nitric oxide (NO) release. Notably, these reactive phenotypes only moderately alter intrinsic neuronal excitability and gamma oscillations (30–100 Hz), which emerge from precise synaptic communication of glutamatergic pyramidal cells and fast-spiking, parvalbumin-positive GABAergic interneurons, in local hippocampal networks. Short-term synaptic plasticity and extracellular potassium homeostasis during neural excitation, also reflecting astrocyte function, are unaffected. In contrast, the coactivation of TLR4 and IFN-γ receptors results in neuronal dysfunction and death, caused mainly by enhanced microglial inducible nitric oxide synthase (iNOS) expression and NO release, because iNOS inhibition is neuroprotective. Thus, activation of TLR4 in microglia in situ requires concomitant IFN-γ receptor signaling from peripheral immune cells, such as T helper type 1 and natural killer cells, to unleash neurotoxicity and inflammation-induced neurodegeneration. Our findings provide crucial mechanistic insight into the complex process of microglia activation, with relevance to several neurologic and psychiatric disorders.Microglia are tissue-resident macrophages in the CNS that become activated in most brain disorders, such as bacterial meningoencephalitis, multiple sclerosis, and Alzheimer’s disease (1, 2). Activation of microglia features changes in morphology and receptor expression, antigen presentation, cytokine release, migration, and phagocytosis, and it ranges from proinflammatory and potentially neurotoxic to anti-inflammatory and neuroprotective phenotypes (1, 3, 4). The mechanisms that control the transition of microglia to reactive phenotypes, including the impact on neuronal function, are mostly unknown, however (5–7).Sensing of microbial or modified endogenous ligands by microglia is mediated by innate pattern recognition receptors, such as scavenger receptors and Toll-like receptors (TLRs). A prime example is TLR4, which acts with CD14, MD-2, and lipopolysaccharide (LPS)-binding protein in recognizing LPS, a cell wall component of Gram-negative bacteria (8, 9). TLR4 is also central to microglial recognition of amyloid-β peptide, which is thought to be part of the inflammatory response in Alzheimer’s disease (7, 10).LPS has been widely used to study the molecular mechanisms of microglial activation in inflammatory neurodegeneration (1–3). In primary monocultures and microglia-neuron cultures, LPS exposure alone or in combination with IFN-γ for a “booster” triggers the massive release of proinflammatory and cytotoxic factors, such as TNF-α, IL-6, and nitric oxide (NO), finally resulting in neuronal death (8, 11–18). Similar effects were observed in vivo after intracerebral administration of LPS (19–21). These and other studies have contributed to the concept that microglial TLR4 activation with LPS (i.e., with a single pathogenic stimulus) is sufficient to induce neurodegeneration (22, 23); however, this concept is biologically risky, and has been questioned in some experimental works and reviews (2–4, 11, 24, 25).Most previous studies focused on two aspects of microglial TLR4 activation with LPS: (i) the properties of the reactive microglial phenotype(s) and (ii) the degree of neurodegeneration. For this purpose, either simple culture systems or in vivo models, in which interactions with leukocytes infiltrating from the blood are inevitable, have been used (1, 4). Thus, it is widely unknown how TLR4 and IFN-γ receptor signaling in microglia individually contribute to neurotoxicity and neurodegeneration in situ. This aspect is highly relevant for several neurologic and psychiatric disorders. Moreover, concomitant alterations in neuronal information processing (i.e., dysfunction in excitatory pyramidal cells and inhibitory GABAergic interneurons, including astrocytes) have been little explored (25–27).We rigorously addressed these fundamental questions in postnatal neuronal tissue (1, 4). To mimic microglial confrontation with LPS in situ and, notably, in the absence of infiltrating leukocytes, we used organotypic hippocampal slice cultures that feature highly preserved cytoarchitectures and complex neuronal network functions (5, 28). Microglial interaction with infiltrating T helper type 1 (Th1) cells and/or natural killer (NK) cells was mimicked by recombinant IFN-γ administration.     

Regulation by a chaperone improves substrate selectivity during cotranslational protein targeting

The ribosome exit site is a crowded environment where numerous factors contact nascent polypeptides to influence their folding, localization, and quality control. Timely and accurate selection of nascent polypeptides into the correct pathway is essential for proper protein biogenesis. To understand how this is accomplished, we probe the mechanism by which nascent polypeptides are accurately sorted between the major cotranslational chaperone trigger factor (TF) and the essential cotranslational targeting machinery, signal recognition particle (SRP). We show that TF regulates SRP function at three distinct stages, including binding of the translating ribosome, membrane targeting via recruitment of the SRP receptor, and rejection of ribosome-bound nascent polypeptides beyond a critical length. Together, these mechanisms enhance the specificity of substrate selection into both pathways. Our results reveal a multilayered mechanism of molecular interplay at the ribosome exit site, and provide a conceptual framework to understand how proteins are selected among distinct biogenesis machineries in this crowded environment.Proper protein biogenesis is a prerequisite for the maintenance of a functional proteome. Accumulating data indicate that this process begins at the ribosome exit site, where many protein biogenesis machineries can interact and gain access to the nascent polypeptide. This includes chaperones (1–5) such as trigger factor (TF) (1, 4, 6, 7), Hsp70, and the nascent polypeptide-associated complex (8–13); modification enzymes (10, 14–16) such as N-acetyl transferase, methionine aminopeptidase, and arginyl transferase; protein-targeting and translocation machineries such as signal recognition particle (SRP) (17–20), SecA (21), the SecYEG (or Sec61p) (22, 23) and YidC translocases (24, 25), and the ribosome-bound quality control complex (26–30). Engagement of these factors with nascent polypeptides influences their folding, assembly, localization, processing, and quality control. Within seconds after the nascent polypeptide emerges from the ribosomal exit tunnel, it must engage the correct set of factors and thus commit to the proper biogenesis pathway. How this is accomplished in the crowded environment at the ribosome exit site is an emerging question. In this work, we address this question by deciphering how nascent proteins are selected between two major protein biogenesis machineries in bacteria, SRP and TF.SRP is a universally conserved ribonucleoprotein complex responsible for the cotranslational targeting of proteins to the eukaryotic endoplasmic reticulum (ER), or the bacterial plasma membrane (31). SRP recognizes ribosome-nascent chain complexes (termed RNC or cargo) carrying strong signal sequences and delivers them to the SecYEG or YidC translocation machinery on the target membrane. SRP binds RNC via two interactions: a helical N domain in the SRP54 protein (called Ffh in bacteria) binds the ribosomal protein L23, and a methionine-rich M domain binds hydrophobic signal sequences on nascent proteins as they emerge from the translating ribosome (Fig. 1A). Both SRP and SRP receptor (called FtsY in bacteria) also contain a conserved NG domain, comprised of a GTPase (guanosine 5′-triphosphate hydrolase) G domain and the N domain, whose direct interaction mediates the delivery of cargo to the target membrane.Open in a separate windowFig. 1.TF binds to SRP-occupied RNCs and weakens SRP binding. (A) Schematic depiction of the FRET assay to measure RNC–SRP binding. Green dot denotes Cm (donor); red dot denotes BODIPY FL (acceptor). (B) N-terminal sequences of the different substrates used in this study. Bold highlights the hydrophobic core of the signal sequences. Asterisk denotes the position where the amino acid is replaced by the Cm dye. (C and D) Equilibrium titrations for RNC–SRP binding in the presence of increasing TF concentration (indicated as increasing shades of red). The data were fitted to Eq. S2 and yielded the following parameters. (C) Apparent K_d values for RNC_FtsQ binding of 1.1 nM, 1.5 nM, 9.2 nM, and 16.6 nM and FRET end points of 0.54, 0.35, 0.29, and 0.17, respectively, with 0 µM, 1 µM, 5 µM, and 30 µM TF present. (D) Apparent K_d values for RNC_phoA binding of 17.2 nM, 21.1 nM, 30.3 nM, 28.3 nM, 31.5 nM, 104.5 nM, 106.3 nM, and 131.9 nM and FRET end points of 0.40, 0.41, 0.39, 0.29, 0.21, 0.19, 0.09, and 0.08, respectively, with 0 µM, 0.1 µM, 0.2 µM, 0.5 µM, 1 µM, 2 µM, 5 µM, and 10 µM TF present. (E) Summary of the effect of TF on apparent RNC–SRP binding affinity with the different substrates. The red dashed line denotes the cellular SRP concentration. Error bars are shown but may not be visible. Error bars are SDs from two to three measurements.Biophysical analyses (32–34) showed that membrane targeting is a two-step process in which SRP and FtsY first associate via their N domains to form a transient early intermediate (31, 32, 35). GTP (guanosine 5′-triphosphate)-driven rearrangements then bring the G domains of both proteins into close contact, giving a stable closed complex (36, 37). This rearrangement also exposes a membrane-binding helix of FtsY and thus is coupled to the membrane targeting of cargo (38). Importantly, SRP•FtsY assembly contributes extensively to the fidelity of SRP (39). The initial recognition of RNC by SRP is insufficient to reject suboptimal cargos bearing weak signal sequences (40, 41). Instead, a correct cargo strongly stabilizes the otherwise labile early intermediate and thus accelerates formation of the SRP•FtsY closed complex over 10³-fold, whereas suboptimal cargos provide much less stimulation (34, 40, 42). This enables rapid delivery of the correct cargos to the target membrane and provides kinetic discrimination against suboptimal cargos (Fig. S1).TF is a major cotranslational chaperone in bacteria, with an estimated cellular concentration of 50–80 µM (6). With a dissociation constant (K_d) of ∼1 µM for ribosomes (43), TF is bound to virtually every ribosome in the cell. Like SRP, TF contacts the ribosome via the L23 and L29 proteins near the ribosome exit site (3, 5, 44). Also analogous to SRP, TF preferentially interacts with hydrophobic sequences on the nascent polypeptide (1, 2, 4, 45, 46), mediated by a large concave surface rich in hydrophobic residues (1, 3–6). Despite these similarities with SRP, TF directs substrate proteins to distinct biogenesis pathways: It exhibits synthetic lethality with DnaK/J and facilitates the productive folding of cytosolic proteins (1, 4, 7, 9, 11). It also interacts with a subset of secretory and outer membrane proteins and interfaces with the posttranslational SecA/B pathway (8, 10, 12–14).SRP and TF are two distinct biogenesis pathways that a nascent protein must commit to. This raises intriguing questions: How do these two factors, which have overlapping substrate preferences, compete and/or collaborate at the ribosome exit site? How are nascent proteins sorted between them and committed to the correct pathway in a timely and accurate manner? Extensive past work to address these questions has led to different (and sometimes contradictory) models, including (i) TF and SRP compete for binding to the RNC (10, 15, 16, 18); (ii) TF and SRP can bind to the same RNC simultaneously (17, 19–21); (iii) FtsY rejects TF from SRP-bound ribosomes (17); and (iv) TF preferentially occupies longer nascent chains (13, 45–47) and, by inference, SRP preferentially binds short nascent chains. A unifying model that reconciles all these observations and explains how nascent chains on the ribosome are selected by TF or SRP is still lacking. Most importantly, most of the previous studies have focused on the initial binding of SRP or TF to the nascent polypeptide, which may not be the step at which nascent proteins are committed to their respective biogenesis pathways.In this work, we used high-resolution biochemical and biophysical analyses to investigate the interplay between TF and SRP at the ribosome exit site in molecular detail. We show that TF regulates SRP function by three distinct mechanisms, which together enhance the ability of the SRP pathway to reject suboptimal substrates. Our results establish a comprehensive and cohesive model that explains previous observations, delineates the complex interplay between protein biogenesis factors at the ribosome exit site, and provides a conceptual foundation to understand how timely and accurate selection of substrates is achieved in this crowded environment.