Identification of Critical Residues of the MyD88 Death Domain Involved in the Recruitment of Downstream Kinases

MyD88 couples the activation of the Toll-like receptors and interleukin-1 receptor superfamily with intracellular signaling pathways. Upon ligand binding, activated receptors recruit MyD88 via its Toll-interleukin-1 receptor domain. MyD88 then allows the recruitment of the interleukin-1 receptor-associated kinases (IRAKs). We performed a site-directed mutagenesis of MyD88 residues, conserved in death domains of the homologous FADD and Pelle proteins, and analyzed the effect of the mutations on MyD88 signaling. Our studies revealed that mutation of residues 52 (MyD88_E52A) and 58 (MyD88_Y58A) impaired recruitment of both IRAK1 and IRAK4, whereas mutation of residue 95 (MyD88_K95A) only affected IRAK4 recruitment. Since all MyD88 mutants were defective in signaling, recruitment of both IRAKs appeared necessary for activation of the pathway. Moreover, overexpression of a green fluorescent protein (GFP)-tagged mini-MyD88 protein (GFP-MyD88-(27–72)), comprising the Glu⁵² and Tyr⁵⁸ residues, interfered with recruitment of both IRAK1 and IRAK4 by MyD88 and suppressed NF-κB activation by the interleukin-1 receptor but not by the MyD88-independent TLR3. GFP-MyD88-(27–72) exerted its effect by titrating IRAK1 and suppressing IRAK1-dependent NF-κB activation. These experiments identify novel residues of MyD88 that are crucially involved in the recruitment of IRAK1 and IRAK4 and in downstream propagation of MyD88 signaling.MyD88 was first discovered during studies addressing the differentiation of mouse myeloid cells in response to growth-inhibitory stimuli (1). Subsequent investigations revealed that MyD88 possesses a modular organization (2), with an amino-terminal death domain (DD),³ found in proteins involved in cell death (3, 4), and a carboxyl-terminal Toll-interleukin-1 receptor (TIR) domain, present in the intracytoplasmic tail of receptors belonging to the Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) superfamily (5). MyD88 also has an intermediate domain (ID) that is crucial in TLR signaling due to its interaction with IRAK4 (6). The role of MyD88 as a signal transducer was first shown in the pathways triggered by the activation of IL-1R (7, 8) and TLR4 (9). Further studies showed that all TLRs, with the sole exception of TLR3, and the IL-1R family utilize the adaptor protein MyD88 to initiate their signaling pathway (10).By virtue of its modular organization, MyD88 critically bridges activated receptor complexes to downstream adaptors/effectors. Upon activation, MyD88 is recruited through its TIR domain by the homologous domain of the activated TLR/IL-1R (11, 12). MyD88, in turn, has been shown to interact with a family of downstream kinases, namely IRAK1 (13), IRAK2 (7), IRAK-M (15), and IRAK4 (16), through the interaction of its DD with the respective DDs present in the amino-terminal region of IRAKs (17). At this stage, this multimeric complex is competent to elicit the propagation of the signal downstream of the receptor(s). Although MyD88 recruits IRAK-1 via DD-DD interactions, its recruitment of IRAK-4 appears to be rather unusual. Burns et al. (6) first demonstrated that an alternatively spliced variant of MyD88 (MyD88s), lacking the ID domain, failed to interact with IRAK-4, suggesting that residues located in both the DD and ID of MyD88 are crucially involved in the recruitment of IRAK-4. Nevertheless, no information is available on the specific residues in the DD in MyD88 required for its interaction with either IRAK1 or IRAK4.The DD was initially defined as the region of homology between the cytoplasmic tails of the FAS/Apo1/CD95 and TNF receptors required for their induction of cytotoxic signaling (18, 19). In analogy with other DD-containing proteins, this domain in MyD88 is also involved in the formation of homomeric and heteromeric interactions. Herein, we have undertaken an alanine-scanning mutational analysis to identify amino acids that are required for downstream signaling and might participate in the homomeric and heteromeric interactions. Our studies revealed that MyD88_E52A and MyD88_Y58A mutants are strongly impaired in the recruitment of both IRAK1 and IRAK4, whereas the MyD88_K95A mutant is deficient in recruiting IRAK4. These findings identify residues within the DD of MyD88 crucially involved in the formation of higher order complexes containing IRAK1 and IRAK4 and required for the propagation of the TLR/IL1-R signaling pathways.     

Lipopolysaccharide-driven Th2 Cytokine Production in Macrophages Is Regulated by Both MyD88 and TRAM

Gram-negative bacterial lipopolysaccharide (LPS) activates macrophages by interacting with Toll-like receptor 4 (TLR4) and triggers the production of various pro-inflammatory Th1 type (type 1) cytokines such as IFNγ, TNFα, and IL8. Though some recent studies cited macrophages as potential sources for Th2 type (type 2) cytokines, little however is known about the intracellular events that lead to LPS-induced type 2 cytokines in macrophages. To understand the mechanisms by which LPS induces type 2 cytokine gene expression, macrophages were stimulated with LPS, and the expression of IL-4 and IL-5 genes were examined. LPS, acting through TLR4, activates both type 1 and type 2 cytokine production both in vitro and in vivo by using macrophages from C3H/HeJ or C3H/HeOuJ mice. Although the baseline level of both TNFα and IL-4 protein was very low, TNFα was released rapidly after stimulation (within 4 h); however, IL-4 was released after 48 h LPS stimulation in secreted form. Silencing of myeloid differentiation protein (MyD88) and TRIF-related adaptor molecule (TRAM), using small interfering RNA abolished IL-4 induction induced by LPS whereas silencing of TRAM has no effect on TNFα induction, thereby indicating that LPS-induced TNFα is MyD88-dependent but IL-4 is required both MyD88 and TRAM. These findings suggest a novel function of LPS and the signaling pathways in the induction of IL-4 gene expression.Pathogen-associated molecular patterns (PAMPs)² such as bacterial LPS are powerful activators of the innate immune system. Exposure to LPS induces an inflammatory reaction in the lung, mediated primarily by an array of inflammatory chemokines and cytokines released by blood monocytes and alveolar macrophages. Mammalian Toll-like receptors (TLRs) are key molecules for recognizing microbial PAMPs and transducing the subsequent inflammatory response (1). LPS is well known to interact with macrophages via TLR4 receptor resulting in cellular activation and synthesis and release of type 1 proinflammatory cytokines such as IFNγ, IL-2, and TNFα (2, 3). These cytokines can further activate monocytes, neutrophils, and lymphocytes, initiating cellular injury and tissue damage (4, 5).Inhaled LPS signaling through TLR4 has also been shown to be necessary to induce type 2 responses to inhaled antigens in a mouse model of allergic asthma (6). IL-4, the prototypic type 2 cytokine, is a pleiotropic cytokine with regulatory effects on B cell growth, T cell growth, and function, immunoglobulin class switching to IgE during the development of immune responses (7). It is also involved in promoting cellular inflammation in the asthmatic lung and contributes to the pathogenesis of allergy and lung remodeling in chronic asthma (8, 9). Different cell types have been reported to produce IL-4 including the well known CD4+ and CD8+ T cells (10, 11), basophils (12), natural killer cells (13), mast cells (14), and eosinophils (15). Pouliot et al. (3) have shown that human alveolar macrophages (AMs) can produce IL-4 in response to PMA and calcium ionophore A23187, and they suggest that AMs might play a crucial role in the type 1/type 2 balance in the lung.LPS-stimulated production of type 1 cytokines such as TNFα and INFγ has been extensively studied in macrophages; however, LPS-stimulated production of type 2 cytokines by macrophages has not yet been well defined. Because the presence of IL-4 at the site of a developing immune response can skew the ultimate cytokine pattern, alveolar macrophage produced IL-4 may be important in the development of allergic airway disease. Indeed, TLR4-defective mice studied using a standard murine model of allergic airway inflammation had an overall decrease in lung inflammatory responses, a dramatic reduction of eosinophils and lymphocytes, and lower circulating levels of OVA-specific IgE (16).The intracellular events following LPS stimulation of TLR4 depends on different sets of Toll/interleukin-1 resistance (TIR) domain containing adaptor molecules. These adaptors provide a structural platform for the recruitment of downstream effector molecules (17, 18). Two distinct responses following engagement of TLR4 with LPS have been described. An early response leading to activation of NF-κB is dependent on MyD88, while a late response utilizes TIR domain-containing adaptor-inducing interferon-γ (TRIF) and TRIF-related adaptor molecule (TRAM) to activate NF-κB (19). While TRIF is common to both TLR3 and TLR4 pathways, TRAM is highly specific for TLR4 (20). The complex signaling network initiated by the interaction of the adaptor and effector proteins ultimately decides the specific pattern of gene expression that is elicited in response to TLR agonists and the particular type of cytokine that is produced determines the recruitment and activation of other immune cells. Therefore, further clarification of the cellular responses following the activation of TLR is crucial and fundamental to our understanding of immune responses.In this report, we show that LPS can stimulate de novo IL-4 gene expression in murine macrophages, both in vitro and in vivo. Utilizing RNA interference we further showed that the induction of IL-4 is both MyD88- and TRAM-dependent (MyD88-independent), while LPS-induced TNFα is strictly dependent on MyD88. These results indicate that LPS induces IL-4 production by macrophages, and provide a new molecular mechanism controlling the regulation of IL-4 prior to the emergence of a polarized adaptive immune response.     

An Oligomeric Signaling Platform Formed by the Toll-like Receptor Signal Transducers MyD88 and IRAK-4

Toll-like receptors (TLRs) mediate responses to pathogen-associated molecules as part of the vertebrate innate immune response to infection. Receptor dimerization is coupled to downstream signal transduction by the recruitment of a post-receptor complex containing the adaptor protein MyD88 and the IRAK protein kinases. In this work, we show that the death domains of human MyD88 and IRAK-4 assemble into closed complexes having unusual stoichiometries of 7:4 and 8:4, the Myddosome. Formation of the Myddosome is likely to be a key event for TLR4 signaling in vivo as we show here that pathway activation requires that the receptors cluster into lipid rafts. Taken together, these findings indicate that TLR activation causes the formation of a highly oligomeric signaling platform analogous to the death-inducing signaling complex of the Fas receptor pathway.In vertebrates, the initial responses of innate immunity are mediated by a family of pattern recognition receptors, which are able to sense the presence of a variety of microbial products such as lipids and non-self nucleic acid (1). One important family of pattern recognition receptors is the Toll-like receptors (TLRs)⁴ that are expressed by many immune system cell types such as macrophages and dendritic cells. TLRs are class one transmembrane receptors that are activated by a process of stimulus-induced dimerization of their extracellular domains. This in turn causes the cytoplasmic Toll/interleukin-1 (IL-1) domains (TIRs) to dimerize, forming a scaffold for the recruitment of downstream signaling components (2). TLRs use five signaling adaptor proteins to couple receptor activation to downstream signal transduction (3). All of these adaptors have TIRs and engage with the activated TLRs by TIR-TIR interactions.One of the adaptor proteins, MyD88, is of particular importance because it is used by all but one of the TLRs as well as by the IL-1 and interferon-γ receptors. MyD88-deficient mice have profoundly impaired innate immune responses and are susceptible to a wide range of infectious diseases. The MyD88 sequence is tripartite and is comprised of a death domain (DD) at the N terminus, a short (40-amino-acid) intermediate domain (ID) of unknown structure, and a C-terminal TIR. Evidence from yeast two-hybrid experiments suggests that MyD88 can self-associate with contacts in both the DD and the TIR (4). The current view of post-receptor signal transduction is that two MyD88 TIR domains bind to the activated TLR, and this enables the recruitment of the protein kinases IRAK-4 and IRAK-1 (5). These kinases have DDs at their N termini, and both are recruited into a complex with MyD88 after signal initiation. It appears that IRAK-4 is recruited first, and this binding requires the ID of MyD88 (6, 7). Thus MyD88s, a splice variant that lacks the ID, down-regulates TLR signaling and cannot recruit IRAK-4 into the post-receptor complex. In contrast, IRAK-1 interacts with MyD88s presumably by DD-DD rather than DD-ID interactions. The next step in the signaling process is for IRAK-4 to phosphorylate IRAK-1, causing activation of the latter and hyper-autophosphorylation. IRAK-1 then dissociates from the complex and interacts with the ubiquitin-protein isopeptide ligase (E3) TRAF6 (8, 9).DDs together with the structurally related caspase recruitment domains (CARDs) and death effector domains (DEDs) form the death domain superfamily (10). There are 215 proteins encoded by the human genome that are predicted to have this fold, and they are widely used in cellular signaling including the TLR and apoptotic pathways. Structurally, DDs contain six antiparallel α-helices, and they are predominantly involved in protein-protein interactions with other DDs. Three modes of DD-DD interaction, types 1, 2, and 3 (10), have been characterized and are illustrated by the structures of the Drosophila Tube-Pelle heterodimer (11), the Procaspase-9 homodimer (12), and most remarkably, by the PIDDosome (13). In the latter case, PIDD, RAIDD, and Caspase-2 form a complex, which results in the proximity-induced activation of Caspase-2 protease activity, which in turn leads to cytochrome c release and apoptotic cell death. The DDs of PIDD and RAIDD interact to produce a complex having a stoichiometry of 5:7, and the subunits are arranged in three layers with five PIDDs, five RAIDDs, and then two RAIDDs. The structure is stabilized by 25 DD-DD contacts of which six are type 2, nine are type 1, and 10 are type 3.In this study, we report that like PIDD and RAIDD, the DDs of human MyD88 and IRAK-4 assemble into defined structures having stoichiometries of 7:4 and 8:4. We propose that the structure has two layers with a ring of seven or eight MyD88 subunits and a second layer of four IRAK-4 subunits. The formation of these higher order assemblies provides insight into the complex regulation and cross-talk observed in the TLR signaling pathways.     

Fatty Acids Modulate Toll-like Receptor 4 Activation through Regulation of Receptor Dimerization and Recruitment into Lipid Rafts in a Reactive Oxygen Species-dependent Manner

The saturated fatty acids acylated on Lipid A of lipopolysaccharide (LPS) or bacterial lipoproteins play critical roles in ligand recognition and receptor activation for Toll-like Receptor 4 (TLR4) and TLR2. The results from our previous studies demonstrated that saturated and polyunsaturated fatty acids reciprocally modulate the activation of TLR4. However, the underlying mechanism has not been understood. Here, we report for the first time that the saturated fatty acid lauric acid induced dimerization and recruitment of TLR4 into lipid rafts, however, dimerization was not observed in non-lipid raft fractions. Similarly, LPS and lauric acid enhanced the association of TLR4 with MD-2 and downstream adaptor molecules, TRIF and MyD88, into lipid rafts leading to the activation of downstream signaling pathways and target gene expression. However, docosahexaenoic acid (DHA), an n-3 polyunsaturated fatty acid, inhibited LPS- or lauric acid-induced dimerization and recruitment of TLR4 into lipid raft fractions. Together, these results demonstrate that lauric acid and DHA reciprocally modulate TLR4 activation by regulation of the dimerization and recruitment of TLR4 into lipid rafts. In addition, we showed that TLR4 recruitment to lipid rafts and dimerization were coupled events mediated at least in part by NADPH oxidase-dependent reactive oxygen species generation. These results provide a new insight in understanding the mechanism by which fatty acids differentially modulate TLR4-mediated signaling pathway and consequent inflammatory responses which are implicated in the development and progression of many chronic diseases.Toll-like receptors (TLRs)³ are one of the key pattern recognition receptor families that play a critical role in inducing innate and adaptive immune responses in mammals by recognizing conserved pathogen-associated molecular pattern of invading microbes. So far, at least thirteen TLRs have been identified in mammalian species (1, 2).Lipopolysaccharide (LPS) from Gram-negative bacteria is the ligand for the TLR4 complex (3), whereas, TLR2 can recognize lipoproteins/lipopeptides of Gram-positive bacteria and mycoplasma (1, 2). LPS forms a complex with LPS-binding protein in serum leading to the conversion of oligomeric micelles of LPS to monomers, which are delivered to CD14. Monomeric LPS is known to bind TLR4/MD-2/CD14 complex (4). Lipid A, which possesses most of the biological activities of LPS, is acylated with hydroxy saturated fatty acids. The 3-hydroxyl groups of these saturated fatty acids are further 3-Ο-acylated by saturated fatty acids. Removal of these Ο-acylated saturated fatty acids from Lipid A not only results in complete loss of endotoxic activity, but also makes Lipid A act as an antagonist against the native Lipid A (5, 6). One or more Lipid As containing unsaturated fatty acids are known to be non-toxic and act as an antagonist against endotoxin (7, 8). In addition, deacylated lipoproteins are unable to activate TLR2 and to induce cytokine expression in monocytes (9). Together, these results suggest that saturated fatty acids acylated on Lipid A or bacterial lipoproteins play critical roles in ligand recognition and receptor activation for TLR4 and TLR2. Indeed, it is suggested that the rapid interaction of bacterial lipopeptides with plasma membrane of macrophages occurs via insertion of their acylated saturated fatty acids as determined by electron energy loss spectroscopy and freeze-fracture techniques (10, 11). TLR2 can form a heterodimer with TLR1 or TLR6, which can discriminate the molecular structure of triacyl or diacyl lipopeptides (12–14). So far there is no evidence that microbial ligands for other TLRs are acylated by saturated fatty acids.Results from our previous studies demonstrated that saturated fatty acids activate TLR4 and polyunsaturated fatty acids (PUFA) inhibit both saturated fatty acid- and LPS-induced activation of TLR4 (15, 16). In addition, the saturated fatty acid lauric acid potentiates, but the n-3 PUFA docosahexaenoic acid (DHA) inhibits lipopeptide (TLR2 agonist)-induced TLR2 activation (17). Together, these results suggest that both TLR2 and TLR4 signaling pathways and target gene expression are reciprocally modulated by saturated and polyunsaturated fatty acids. However, the mechanism for this modulation by fatty acids is not understood.TLR4 is recruited to lipid raft factions after cells are treated with LPS and subsequently induces tumor necrosis factor-α expression in RAW264.7 cells (18). This process occurs in an ROS-dependent manner because inhibition of NADPH oxidase suppresses TLR4 recruitment to lipid rafts (19). Methyl-β-dextrin, a lipid raft inhibitor, significantly inhibits the LPS-induced expression of cytokine (19), suggesting that lipid rafts are essential for TLR4-mediated signal transduction and target gene expression. Lipid rafts are a collection of lipid membrane microdomains characterized by insolubility in non-ionic detergents. Lipid rafts serve as a platform where receptor-mediated signal transduction is initiated (20). Lipid rafts have a special lipid composition that is rich in cholesterol, sphingomyelin, and glycolipids (21). The polar lipids in detergent-resistant membrane contain predominantly saturated fatty acyl residues with underrepresented PUFAs (22–24), suggesting that saturated fatty acyl chains favor lipid raft association. On the other hand, n-3 PUFAs displace signaling proteins from lipid rafts by altering lipid composition, and the displacement leads to the suppression of T-cell receptor-mediated signaling (25). It is now well documented that TLRs form homo- or hetero-oligomers (1, 2). TLR4 homodimerization is the initial step of the receptor activation. Results from our previous studies suggest that the molecular target by which saturated fatty acids and n-3 PUFAs reciprocally modulate TLR4 activation is the receptor complex itself or the event leading to the receptor activation instead of the downstream signaling components (15, 16). Therefore, we determined whether the reciprocal modulation of TLR4 activation is mediated by regulation of the dimerization and recruitment of TLR4 into lipid rafts, and if these processes occur in an ROS-dependent manner.     

TLR2 Mediates Gap Junctional Intercellular Communication through Connexin-43 in Intestinal Epithelial Barrier Injury

Gap junctional intercellular communication (GJIC) coordinates cellular functions essential for sustaining tissue homeostasis; yet its regulation in the intestine is not well understood. Here, we identify a novel physiological link between Toll-like receptor (TLR) 2 and GJIC through modulation of Connexin-43 (Cx43) during acute and chronic inflammatory injury of the intestinal epithelial cell (IEC) barrier. Data from in vitro studies reveal that TLR2 activation modulates Cx43 synthesis and increases GJIC via Cx43 during IEC injury. The ulcerative colitis-associated TLR2-R753Q mutant targets Cx43 for increased proteasomal degradation, impairing TLR2-mediated GJIC during intestinal epithelial wounding. In vivo studies using mucosal RNA interference show that TLR2-mediated mucosal healing depends functionally on intestinal epithelial Cx43 during acute inflammatory stress-induced damage. Mice deficient in TLR2 exhibit IEC-specific alterations in Cx43, whereas administration of a TLR2 agonist protects GJIC by blocking accumulation of Cx43 and its hyperphosphorylation at Ser³⁶⁸ to prevent spontaneous chronic colitis in MDR1α-deficient mice. Finally, adding the TLR2 agonist to three-dimensional intestinal mucosa-like cultures of human biopsies preserves intestinal epithelial Cx43 integrity and polarization ex vivo. In conclusion, Cx43 plays an important role in innate immune control of commensal-mediated intestinal epithelial wound repair.The intestinal epithelial cell (IEC)³ barrier provides the front line of mucosal host defense in the intestine. The IEC barrier confers anatomic integrity and immunologic protection of the intestinal mucosal surface. Because the IEC barrier constantly faces diverse populations of lumenal microbes and other potential threats, it must exert a highly defined process of continuous discrimination: excluding harmful antigens while allowing host-beneficial substances to permeate (1, 2). Para- and intercellular transit of molecules is modulated by a complex network of closely arranged tight (TJ) and gap junctions (GJ) between juxtaposed IEC. Gap junctional intercellular communication (GJIC) is an essential, but not well understood, mechanism for cellular and tissue homeostasis that coordinates cell-cell passage of ions and small metabolites (<1 kDa). Thus, GJIC regulates cell proliferation, migration, and differentiation (3). GJ channels are formed by hexameric connexins at the plasma membrane. Cx43 is the major connexin and represents a key target in GJIC regulation (4). It is differentially phosphorylated at a dozen or more residues throughout its life cycle (5–9). Alteration of GJIC caused by changes in Cx43 has been proposed to be involved in the pathophysiology of diverse IEC barrier diseases, including inflammatory bowel diseases, necrotizing enterocolitis, cancer, and enteric infection (10–12). However, immune mediators that allow protective GJIC via Cx43 to sustain IEC barrier function during mucosal damage have not yet been identified.Toll-like receptor 2 (TLR2), a member of the TLR family that is constitutively expressed in IEC (13–15), recognizes conserved molecular patterns associated with both Gram-negative and -positive bacteria (16). We have previously shown that commensal-mediated TLR2 helps to maintain functional TJ barrier integrity of the intestinal epithelial layer. TLR2 enhances transepithelial resistance of the IEC barrier by apical redistribution of ZO-1 via protein kinase Cα/δ (17). Treatment with the TLR2 ligand PCSK protects ZO-1-associated IEC barrier integrity and decreases intestinal permeability in acute colitis (18). Previous studies in other cell types have demonstrated that the second PDZ domain of ZO-1 interacts with the carboxyl terminus of Cx43 (19, 20). ZO-1 binds to Cx43 preferentially during the G₀ phase, enhancing assembly and stabilization of GJIC (21, 22). Like TLR2, Cx43 and ZO-1 reside in caveolin-1-associated lipid raft microdomains (23–25). We therefore hypothesized that the binding between ZO-1 and Cx43 may allow TLR2 to control IEC barrier function by GJIC.In this study, we identified a new physiological mechanism of innate immune host defense in the injured intestine. Our findings indicated that Cx43 serves as an important component of the protective innate immune response of the intestinal epithelium. TLR2-induced GJIC via Cx43 appears to control IEC barrier function and restitution during acute and chronic inflammatory damage, enhancing mucosal homeostasis between commensals and host. UC-associated TLR2 mutant results in impaired GJIC by a proteasomal-dependent increase in Cx43 turnover.     

Mycobacterial Phosphatidylinositol Mannosides Negatively Regulate Host Toll-like Receptor 4, MyD88-dependent Proinflammatory Cytokines, and TRIF-dependent Co-stimulatory Molecule Expression

Mycobacterium tuberculosis modulates host immune responses through proteins and complex glycolipids. Here, we report that the glycosylphosphatidylinositol anchor phosphatidyl-myo-inositol hexamannosides PIM₆ or PIM₂ exert potent anti-inflammatory activities. PIM strongly inhibited the Toll-like receptor (TLR4) and myeloid differentiation protein 88 (MyD88)-mediated release of NO, cytokines, and chemokines, including tumor necrosis factor (TNF), interleukin 12 (IL-12) p40, IL-6, keratinocyte-derived chemokine, and also IL-10 by lipopolysaccharide (LPS)-activated macrophages. This effect was independent of the presence of TLR2. PIM also reduced the LPS-induced MyD88-independent, TIR domain-containing adaptor protein inducing interferon β (TRIF)-mediated expression of co-stimulatory receptors. PIM inhibited LPS/TLR4-induced NFκB translocation. Synthetic PIM₁ and a PIM₂ mimetic recapitulated these in vitro activities and inhibited endotoxin-induced airway inflammation, TNF and keratinocyte-derived chemokine secretion, and neutrophil recruitment in vivo. Mannosyl, two acyl chains, and phosphatidyl residues are essential for PIM anti-inflammatory activity, whereas the inosityl moiety is dispensable. Therefore, PIM exert potent antiinflammatory effects both in vitro and in vivo that may contribute to the strategy developed by mycobacteria for repressing the host innate immunity, and synthetic PIM analogs represent powerful anti-inflammatory leads.Multifold interactions between Mycobacterium tuberculosis and host phagocytes determine immune responses to M. tuberculosis and tuberculosis pathogenesis (for review, see Refs. 1 and 2). Alveolar macrophages, the primary host cells for M. tuberculosis, and dendritic cells that carry mycobacterial antigens from the infection site to the draining lymph nodes to establish a T cell-mediated immune response contribute to modulate the innate immune response by secreting cytokines after recognition of microbial motives. Among them, TNF² is an essential mediator for granuloma formation and containment of M. tuberculosis infection. Similarly, IL-12, interferon γ, but also IL-1, IL-18, IL-23, and nitric oxide are required for host defense (1–6). Phagocytes are also a source of immuno-modulatory cytokines, such as IL-10 and transforming growth factor-β, which dampen the immune response and inflammation. Mycobacteria-derived molecules down-modulating the immune system have been described, including the protein ESAT-6, mannose-capped lipoarabinomannan (ManLAM), and lipomannans (LM) (7–12). Here, we report that phosphatidyl-myo-inositol mannosides (PIM), the glycosylphosphatidylinositol (GPI) anchor structure of LAM and LM, exert strong anti-inflammatory activities.Mycobacterial cell wall LAM, LM, and PIM are recognized by macrophages and dendritic cells through various pattern recognition receptors, including Toll-like receptors (TLRs) (13–16) and C-type lectins such as mannose receptor (MR/CD206) and dendritic cell-specific intercellular adhesion molecule-3 grabbing nonintegrin (DC-SIGN/CD209), central to M. tuberculosis binding and internalization by human dendritic cells (17–20). DC-SIGN and mannose receptor were proposed to mediate ManLAM inhibition of LPS-induced IL-12 production in dendritic cells, an activity ascribed to the mannosylated cap (8, 9). We showed recently that mycobacterial LM have a dual potential for pro-inflammatory and anti-inflammatory effects (11), tri- and tetra-acylated LM fractions exerting stimulatory effects through TLR2, TLR4, and MyD88 (21), whereas diacylated LM inhibit LPS-induced cytokine response independently of TLR2, SIGN-R1, and mannose receptor (12).PIM are biosynthetic precursors of LM and LAM (22–25). Dimannoside (PIM₂) and hexamannoside (PIM₆) PIM are the two most abundant classes of PIM found in M. tuberculosis H37Rv and Mycobacterium bovis BCG (see Fig. 1). PIM purification and molecular chemical characterization revealed four major acyl forms, mono- to tetra-acylated (lyso-PIM for one acyl, PIM for two acyl, Ac₁PIM for three acyl, and Ac₂PIM for four acyl, respectively; see Fig. 1) for both PIM₂ and PIM₆ (26–29). Higher order PIM with mannose cap-like structures were found to preferentially associate with human MR and to contribute to phagosome-lysosome fusion (20). The degree of acylation influenced higher order PIM association with the MR, whereas PIM₂ was recognized by DC-SIGN independently of its acylation degree. The complete synthesis of the different PIM has recently been reported (30–33).Open in a separate windowFIGURE 1.Natural PIM and synthetic PIM₁ and PIM₂ mimetics used in the study. Shown is a schematic representation of natural lyso-PIM₆, PIM₆, Ac₁PIM₆, Ac₂PIM₆, and PIM₂ (A) and synthetic PIM₁ (B) showing the C16 and C18 acyl groups on glycerol chain positions sn-2 and sn-1, the precursor PI, a synthetic mimetic of PIM₂ (PIM₂ mimetic) bearing C16 and C18 acyl chains, the de-acylated control molecule precursor of the PIM₂ mimetic (de-AcPIM₂ mimetic), and a PIM₂ mimetic with replacement of the phosphodiester moiety by a carbonate.Here, we analyzed isolated acyl forms of PIM and identified PIM₂ and PIM₆ but also synthetic PIM₁ and a mimetic of PIM₂ as strong inhibitors of endotoxin-induced proinflammatory responses in vitro and in vivo. Using macrophages from genetically modified mice, we characterized PIM inhibitory effects on MyD88, TRIF, and NFκB signaling pathways. Hence, not only complex mycobacterial lipoglycans like ManLAM and LM but also small molecular weight PIM analogues are potent inhibitors of host inflammatory responses.     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]