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1.  Autophagy Genes Enhance Murine Gammaherpesvirus 68 Reactivation From Latency by Preventing Virus-induced Systemic Inflammation 
Cell host & microbe  2016;19(1):91-101.
SUMMARY
Host genes that regulate systemic inflammation upon chronic viral infection are incompletely understood. Murine γ-herpesvirus 68 (MHV68) infection is characterized by latency in macrophages, and reactivation is inhibited by Interferon-γ (IFN-γ). Using a Lysozyme-M-cre (LysMcre) expression system, we show that deletion of autophagy-related (Atg) genes Fip200, beclin 1, Atg14, Atg16L1, Atg7, Atg3, and Atg5, in the myeloid compartment, inhibited MHV68 reactivation in macrophages. Atg5-deficiency did not alter reactivation from B cells, and effects on reactivation from macrophages were not explained by alterations in productive viral replication or the establishment of latency. Rather, chronic MHV68 infection triggered increased systemic inflammation, increased T cell production of IFN-γ and an IFN-γ-induced transcriptional signature in macrophages from Atg gene-deficient mice. The Atg5-related reactivation defect was partially reversed by neutralization of IFN-γ. Thus Atg genes in myeloid cells dampen virus-induced systemic inflammation, creating an environment that fosters efficient MHV68 reactivation from latency.
doi:10.1016/j.chom.2015.12.010
PMCID: PMC4714357  PMID: 26764599
2.  Homeostatic Control of Innate Lung Inflammation by Vici Syndrome Gene Epg5 and Additional Autophagy Genes Promotes Influenza Pathogenesis 
Cell host & microbe  2016;19(1):102-113.
SUMMARY
Mutations in the autophagy gene EPG5 are linked to the multisystem human disease Vici syndrome, which is characterized in part by pulmonary abnormalities, including recurrent infections. We found that Epg5-deficient mice exhibited elevated baseline innate immune cellular and cytokine-based lung inflammation and were resistant to lethal influenza virus infection. Lung transcriptomics, bone marrow transplantation experiments, and analysis of cellular cytokine expression indicated that Epg5 plays a role in lung physiology through its function in macrophages. Deletion of other autophagy genes including Atg14, FIP200, Atg5, and Atg7 in myeloid cells also led to elevated basal lung inflammation and influenza resistance. This suggests that Epg5 and other Atg genes function in macrophages to limit innate immune inflammation in the lung. Disruption of this normal homeostatic dampening of lung inflammation results in increased resistance to influenza, suggesting that normal homeostatic mechanisms that limit basal tissue inflammation support some infectious diseases.
doi:10.1016/j.chom.2015.12.011
PMCID: PMC4714358  PMID: 26764600
3.  Antigen export reduces antigen presentation and limits T cell control of M. tuberculosis 
Cell host & microbe  2016;19(1):44-54.
Persistence of Mycobacterium tuberculosis results from bacterial strategies that manipulate host adaptive immune responses. Infected dendritic cells (DCs) transport M. tuberculosis to local lymph nodes but activate CD4 T cells poorly, suggesting bacterial manipulation of antigen presentation. However, M. tuberculosis antigens are also exported from infected DCs and taken up and presented by uninfected DCs, possibly overcoming this blockade of antigen presentation by infected cells. Here we show that the first stage of this antigen transfer, antigen export, benefits M. tuberculosis by diverting bacterial proteins from the antigen presentation pathway. Kinesin-2 is required for antigen export and depletion of this microtubule-based motor increases activation of antigen-specific CD4 T cells by infected cells and improves control of intracellular infection. Thus, although antigen transfer enables presentation by bystander cells, it does not compensate for reduced antigen presentation by infected cells and represents a bacterial strategy for CD4 T cell evasion.
Graphical abstract
Antigen export: In M. tuberculosis-infecfed cells, bacterial antigens are exported by kinesin 2-dependent vesicular transport, which reduces the quantity of antigen routed to the MHC class II antigen presentation pathway. Sub-optimal antigen presentation limits CD4 T ceil activation by infected cells.
Blockade of antigen export: Depletion of kinesin 2 from M. tuberculosis-infected cells decreases antigen export. More antigen is available to the MHC class II antigen presentation pathway, resulting in more effective CD4 T cell activation by infected cells.
doi:10.1016/j.chom.2015.12.003
PMCID: PMC4715867  PMID: 26764596
4.  Structural Insight into Polymorphic ABO Glycan Binding by Helicobacter pylori 
Cell host & microbe  2016;19(1):55-66.
Summary
The Helicobacter pylori adhesin BabA binds mucosal ABO/Leb blood group (bg) carbohydrates. BabA facilitates bacterial attachment to gastric surfaces, increasing strain virulence and forming a recognized risk factor for peptic ulcers and gastric cancer. High sequence variation causes BabA functional diversity, but the underlying structural-molecular determinants are unknown. We generated X-ray structures of representative BabA isoforms that reveal a polymorphic, three-pronged Leb binding site. Two diversity loops, DL1 and DL2, provide adaptive control to binding affinity, notably ABO versus O bg preference. H. pylori strains can switch bg preference with single DL1 amino acid substitutions, and can coexpress functionally divergent BabA isoforms. The anchor point for receptor binding is the embrace of an ABO fucose residue by a disulfide-clasped loop, which is inactivated by reduction. Treatment with the redox-active pharmaceutic N-acetylcysteine lowers gastric mucosal neutrophil infiltration in H. pylori-infected Leb-expressing mice, providing perspectives on possible H. pylori eradication therapies.
Graphical abstract
doi:10.1016/j.chom.2015.12.004
PMCID: PMC4793151  PMID: 26764597
5.  Genetic and metabolic signals during acute enteric bacterial infection alter the microbiota and drive progression to chronic inflammatory disease 
Cell host & microbe  2016;19(1):21-31.
Summary
Chronic inflammatory disorders are thought to arise due to an interplay between predisposing host genetics and environmental factors. For example, the onset of inflammatory bowel disease is associated with enteric proteobacterial infection, yet the mechanistic basis for this association is unclear. We have shown previously that genetic defiency in TLR1 promotes acute enteric infection by the proteobacteria Yersinia enterocolitica. Examining that model further, we uncovered an altered cellular immune response that promotes the recruitment of neutrophils which in turn increases metabolism of the respiratory electron acceptor tetrathionate by Yersinia. These events drive permanent alterations in anti-commensal immunity, microbiota composition and chronic inflammation, which persist long after Yersinia clearence. Deletion of the bacterial genes involved in tetrathionate respiration or treatment using a targeted probiotics could prevent microbiota alterations and inflammation. Thus, acute infection can drive long term immune and microbiota alterations leading to chronic inflammatory disease in genetic predisposed individuals.
doi:10.1016/j.chom.2015.12.006
PMCID: PMC4839196  PMID: 26764594
6.  The Host Shapes the Gut Microbiota via Fecal microRNA 
Cell host & microbe  2016;19(1):32-43.
SUMMARY
The host gut microbiota varies across species and individuals but is relatively stable over time within an individual. How the host selectively shapes the microbiota is largely unclear. Here, we show that fecal microRNA (miRNA)-mediated inter-species gene regulation facilitates host control of the gut microbiota. MiRNAs are abundant in mouse and human fecal samples and present within extracellular vesicles. Cell-specific loss of the miRNA-processing enzyme, Dicer, identified intestinal epithelial cells (IEC) and Hopx-positive cells as predominant fecal miRNA sources. These miRNAs can enter bacteria, such as F. nucleatum and E. coli, specifically regulate bacterial gene transcripts and affect bacterial growth. IEC-miRNA deficient (Dicer1ΔIEC) mice exhibit uncontrolled gut microbiota and exacerbated colitis and WT fecal miRNA transplantation restores fecal microbes and ameliorates colitis. These findings identify both a physiologic role by which fecal miRNA shapes the gut microbiota and a potential strategy for manipulating the microbiome.
Graphical Abstract
doi:10.1016/j.chom.2015.12.005
PMCID: PMC4847146  PMID: 26764595
7.  Noncanonical Fungal Autophagy Inhibits Inflammation in Response to IFN-γ via DAPK1 
Cell Host & Microbe  2016;20(6):744-757.
Summary
Defects in a form of noncanonical autophagy, known as LC3-associated phagocytosis (LAP), lead to increased inflammatory pathology during fungal infection. Although LAP contributes to fungal degradation, the molecular mechanisms underlying LAP-mediated modulation of inflammation are unknown. We describe a mechanism by which inflammation is regulated during LAP through the death-associated protein kinase 1 (DAPK1). The ATF6/C/EBP-β/DAPK1 axis activated by IFN-γ not only mediates LAP to Aspergillus fumigatus but also concomitantly inhibits Nod-like receptor protein 3 (NLRP3) activation and restrains pathogenic inflammation. In mouse models and patient samples of chronic granulomatous disease, which exhibit defective autophagy and increased inflammasome activity, IFN-γ restores reduced DAPK1 activity and dampens fungal growth. Additionally, in a cohort of hematopoietic stem cell-transplanted patients, a genetic DAPK1 deficiency is associated with increased inflammation and heightened aspergillosis susceptibility. Thus, DAPK1 is a potential drugable player in regulating the inflammatory response during fungal clearance initiated by IFN-γ.
Graphical Abstract
Highlights
•IFN-γ restrains inflammation during fungal clearance via DAPK1•DAPK1 promotes noncanonical autophagy and NLRP3 proteasomal degradation•DAPK1 deficiency predicts infection and inflammation in CGD or transplanted patients•IFN-γ therapy restores defective DAPK1
Defects in noncanonical autophagy increase inflammatory pathology during fungal infection. Oikonomou et al. find that the kinase DAPK1 induced by IFN-γ promotes both noncanonical autophagy and NLRP3 inflammasome proteasomal degradation in response to Aspergillus fumigatus. By restoring DAPK1, IFN-γ may assist fungal clearance while restraining inflammation in mice and humans.
doi:10.1016/j.chom.2016.10.012
PMCID: PMC5161749  PMID: 27889463
8.  microRNA function is limited to cytokine control in the acute response to virus infection 
Cell host & microbe  2015;18(6):714-722.
SUMMARY
With the capacity to fine-tune protein expression via sequence-specific interactions, microRNAs (miRNAs) help regulate cell maintenance and differentiation. While some studies have also implicated miRNAs as regulators of the antiviral response, others have found that the RISC complex that facilitates miRNA-mediated silencing is rendered non-functional during cellular stress, including virus infection. To determine the global role of miRNAs in the cellular response to virus infection, we generated a vector that rapidly eliminates total cellular miRNA populations in terminally differentiated primary cultures. Loss of miRNAs has a negligible impact on both innate sensing of and immediate response to acute viral infection. In contrast, miRNA depletion specifically enhances cytokine expression, providing a post-translational mechanism for immune cell activation during cellular stress. This work highlights the physiological role of miRNAs during the antiviral response and suggests their contribution is limited to chronic infections and the acute activation of the adaptive immune response.
doi:10.1016/j.chom.2015.11.003
PMCID: PMC4683400  PMID: 26651947
9.  Molecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses 
Cell host & microbe  2015;18(6):705-713.
SUMMARY
In the Western hemisphere, at least five mammarenaviruses cause human viral hemorrhagic fevers with high case fatality rates. Junín virus (JUNV) is the only hemorrhagic fever virus for which transfusion of survivor immune plasma that contains neutralizing antibodies (‘passive immunity’) is an established treatment. Here, we report the structure of the JUNV surface glycoprotein receptor-binding subunit (GP1) bound to a neutralizing monoclonal antibody. The antibody engages the GP1 site that binds transferrin receptor 1 (TfR1) – the host cell surface receptor for all New World hemorrhagic fever mammarenaviruses - and mimics an important receptor contact. We show that survivor immune plasma contains antibodies that bind the same epitope. We propose that viral receptor-binding site accessibility explains the success of passive immunity against JUNV and that this functionally conserved epitope is a potential target for therapeutics and vaccines to limit infection by all New World hemorrhagic fever mammarenaviruses.
doi:10.1016/j.chom.2015.11.005
PMCID: PMC4685251  PMID: 26651946
10.  A single bacterial immune evasion strategy dismantles both MyD88 and TRIF signalling pathways downstream of TLR4 
Cell host & microbe  2015;18(6):682-693.
Summary
During bacterial infections, Toll-like receptor 4 (TLR4) signals through the MyD88-dependent pathway to promote rapid pro-inflammatory responses, but also signals via the TRIF-dependent pathway, which promotes Type-I interferon responses and acts with MyD88 signaling to potentiate inflammatory cytokine production. Bacteria can inhibit the MyD88 pathway, but if the TRIF pathway is also targeted is unclear. We demonstrate that, in addition to MyD88, Yersinia pseudotuberculosis inhibits TRIF signaling through the Type III secretion system effector YopJ. Suppression of TRIF signaling occurs during dendritic cell (DC) and macrophage infection, and prevents expression of Type-I IFN and pro-inflammatory cytokines. YopJ-mediated inhibition of TRIF prevents DCs from inducing Natural Killer cell production of antibacterial interferon-γ. During infection of DCs, YopJ potently inhibits MAPK pathways but does not prevent activation of IKK- or TBK1-dependent pathways. This singular YopJ activity efficiently inhibits TLR4 transcription-inducing activities, thus illustrating a simple means by which pathogens impede innate immunity.
doi:10.1016/j.chom.2015.11.006
PMCID: PMC4685476  PMID: 26651944
11.  Neuronal Stress Pathway Mediating a Histone Methyl/Phospho Switch is Required for Herpes Simplex Virus Reactivation 
Cell host & microbe  2015;18(6):649-658.
SUMMARY
Herpes simplex virus (HSV) reactivation from latent neuronal infection requires stimulation of lytic gene expression from promoters associated with repressive heterochromatin. Various neuronal stresses trigger reactivation, but how these stimuli activate silenced promoters remains unknown. We show that a neuronal pathway involving activation of c-Jun N-terminal kinase (JNK), common to many stress responses, is essential for initial HSV gene expression during reactivation. This JNK activation in neurons is mediated by dual leucine zipper kinase (DLK) and JNK-interacting protein 3 (JIP3), which direct JNK towards stress responses instead of other cellular functions. Surprisingly, JNK-mediated viral gene induction occurs independently of histone demethylases that remove repressive lysine modifications. Rather, JNK signaling results in a histone methyl/phospho switch on HSV lytic promoters, a mechanism permitting gene expression in the presence of repressive lysine methylation. JNK is present on viral promoters during reactivation, thereby linking a neuronal-specific stress pathway and HSV reactivation from latency.
doi:10.1016/j.chom.2015.11.007
PMCID: PMC4681005  PMID: 26651941
12.  Group B Streptococcus evades host immunity by degrading hyaluronan 
Cell host & microbe  2015;18(6):694-704.
SUMMARY
In response to tissue injury, hyaluronan (HA) polymers are cleaved by host hyaluronidases generating small fragments that ligate Toll-Like Receptors to elicit inflammatory responses. Pathogenic bacteria such as Group B Streptococci (GBS) express and secrete hyaluronidases as a mechanism for tissue invasion, but it is not known how this activity relates to immune detection of HA. We found that bacterial hyaluronidases secreted by GBS and other Gram-positive pathogens degrade pro-inflammatory HA fragments to their component disaccharides. Additionally, HA disaccharides block TLR2/4 signaling elicited by both host-derived HA fragments and other TLR2/4 ligands, including LPS. Application of GBS hyaluronidase or HA disaccharides reduced pulmonary pathology and pro-inflammatory cytokine levels in an acute lung injury model. We conclude that breakdown of host-generated pro-inflammatory HA fragments to disaccharides allows bacterial pathogens to evade immune detection and could be exploited as a strategy to treat inflammatory diseases.
doi:10.1016/j.chom.2015.11.001
PMCID: PMC4683412  PMID: 26651945
13.  Evolution and spread of Ebola virus in Liberia, 2014–2015 
Cell host & microbe  2015;18(6):659-669.
SUMMARY
The 2013–present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; however, relatively few sequences have been determined from patients in Liberia, the second worst-affected country. Here, we report 140 EBOV genome sequences from the second wave of the Liberian outbreak and analyze them in combination with 782 previously published sequences from throughout the Western African outbreak. While multiple early introductions of EBOV to Liberia are evident, the majority of Liberian EVD cases are consistent with a single introduction, followed by spread and diversification within the country. Movement of the virus within Liberia was widespread and reintroductions from Liberia served as an important source for the continuation of the already ongoing EVD outbreak in Guinea. Overall, little evidence was found for incremental adaptation of EBOV to the human host.
doi:10.1016/j.chom.2015.11.008
PMCID: PMC4711363  PMID: 26651942
14.  Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding 
Cell host & microbe  2015;18(6):723-735.
SUMMARY
Several systems-level datasets designed to dissect host-pathogen interactions during influenza A infection have been reported. However, apparent discordance among these data has hampered their full utility toward advancing mechanistic and therapeutic knowledge. To collectively reconcile these datasets, we performed a meta-analysis of data from eight published RNAi screens and integrated these data with three protein interaction datasets, including one generated within the context of this study. Further integration of these data with global virus-host interaction analyses revealed a functionally validated biochemical landscape of the influenza-host interface, which can be queried through a simplified and customizable web portal (http://www.metascape.org/IAV). Follow-up studies revealed that the putative ubiquitin ligase UBR4 associates with the viral M2 protein and promotes apical transport of viral proteins. Taken together, the integrative analysis of influenza OMICs datasets illuminates a viral-host network of high-confidence human proteins that are essential for influenza A virus replication.
Graphical Abstract
doi:10.1016/j.chom.2015.11.002
PMCID: PMC4829074  PMID: 26651948
15.  The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease 
Cell host & microbe  2014;16(3):276-289.
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
doi:10.1016/j.chom.2014.08.014
PMCID: PMC5109542  PMID: 25211071
16.  Normalization of host intestinal mucus layers requires long-term microbial colonization 
Cell host & microbe  2015;18(5):582-592.
SUMMARY
The intestinal mucus layer provides a barrier limiting bacterial contact with the underlying epithelium. Mucus structure is shaped by intestinal location and the microbiota. To understand how commensals modulate gut mucus, we examined mucus properties under germ-free (GF) conditions and during microbial colonization. Although the colon mucus structure of GF mice was similar to conventionally raised (Convr) mice, the GF inner mucus layer was penetrable to bacteria-sized beads. During colonization, in which GF mice were gavaged with Convr microbiota, the small intestine mucus required five weeks to be normally detached and colonic inner mucus six weeks to become impenetrable. The composition of the small intestinal microbiota during colonization was similar to Convr donors until three weeks when Bacteroides increased, Firmicutes decreased, and segmented filamentous bacteria became undetectable. These findings highlight the dynamics of mucus layer development and indicate that studies of mature microbe-mucus interactions should be conducted weeks after colonization.
doi:10.1016/j.chom.2015.10.007
PMCID: PMC4648652  PMID: 26526499
MUC2; Mucin; Mucus; Bacteria; Colonization; Commensals; Colon; Small Intestine; Glycosylation; Glycosyltransferase; Proteomics; Mass Spectrometry
17.  Poorly cross-linked peptidoglycan in MRSA due to mecA induction activates the inflammasome and exacerbates immunopathology 
Cell host & microbe  2015;18(5):604-612.
Summary
Methicillin-resistant S. aureus (MRSA) is a leading health problem. Compared to methicillin-sensitive S. aureus, MRSA infections are associated with greater morbidity and mortality but the mechanisms underlying MRSA pathogenicity are unclear. Here we show that the protein conferring β-lactam antibiotic resistance, penicillin-binding protein 2A (encoded by the mecA gene), directly contributes to pathogenicity during MRSA infection. MecA induction leads to a reduction in peptidoglycan cross-linking that allows for enhanced degradation and detection by phagocytes, resulting in robust IL-1β production. Peptidoglycan isolated from β-lactam-challenged MRSA strongly induces the NLRP3 inflammasome in macrophages but these effects are lost upon peptidoglycan solubilization. Mutant MRSA bacteria with naturally-occurring short peptidoglycan cross-links induce high IL-1β levels in vitro, and cause increased pathology in vivo. β-lactam treatment of MRSA skin infection exacerbates immunopathology, which is IL-1-dependent. Thus, antibiotic-induced expression of mecA during MRSA skin infection contributes to immunopathology by altering peptidoglycan structure.
Graphical Abstract
doi:10.1016/j.chom.2015.10.011
PMCID: PMC4648675  PMID: 26567511
18.  Microbiota-dependent priming of antiviral intestinal immunity in Drosophila 
Cell host & microbe  2015;18(5):571-581.
Summary
Enteric pathogens must overcome intestinal defenses to establish infection. In Drosophila, the ERK signaling pathway inhibits enteric virus infection. The intestinal microflora also impacts immunity but its role in enteric viral infection is unknown. Here we show that two signals are required to activate antiviral ERK signaling in the intestinal epithelium. One signal depends on recognition of peptidoglycan from the microbiota, particularly from the commensal Acetobacter pomorum, which primes the NF-kB-dependent induction of a secreted factor, Pvf2. However, the microbiota is not sufficient to induce this pathway; a second virus-initiated signaling involving release of transcriptional paused genes mediated by the kinase Cdk9 is also required for Pvf2 production. Pvf2 stimulates antiviral immunity by binding to the receptor tyrosine kinase PVR, which is necessary and sufficient for intestinal ERK responses. These findings demonstrate that sensing of specific commensals primes inflammatory signaling required for epithelial responses that restrict enteric viral infections.
Graphical Abstract
doi:10.1016/j.chom.2015.10.010
PMCID: PMC4648705  PMID: 26567510
19.  CDK11 in TREX/THOC regulates HIV mRNA 3’ end processing 
Cell host & microbe  2015;18(5):560-570.
SUMMARY
Transcriptional cyclin-dependent kinases play important roles in eukaryotic gene expression. CDK7, CDK9 (P-TEFb) and CDK13 are also critical for HIV replication. However, the function of CDK11 remained enigmatic. In this report, we determined that CDK11 regulates the cleavage and polyadenylation (CPA) of all viral transcripts. CDK11 was found associated with the TREX/THOC, which recruited this kinase to DNA. Once at the viral genome, CDK11 phosphorylated serines at position 2 in the CTD of RNAPII, which increased levels of CPA factors at the HIV 3’ end. In its absence, cleavage of viral transcripts was greatly attenuated. In contrast, higher levels of CDK11 increased the length of HIV polyA tails and the stability of mature viral transcripts. We conclude that CDK11 plays a critical role for the co-transcriptional processing of all HIV mRNA species.
doi:10.1016/j.chom.2015.10.012
PMCID: PMC4648707  PMID: 26567509
20.  Filamentous Bacteriophage Promote Biofilm Assembly And Function 
Cell host & microbe  2015;18(5):549-559.
Summary
Biofilms - communities of bacteria encased in a polymer-rich matrix- confer bacteria with the ability to persist in pathologic host contexts, such as the cystic fibrosis (CF) airways. How bacteria assemble polymers into biofilms is largely unknown. We find that the extracellular matrix produced by Pseudomonas aeruginosa self-assembles into a liquid crystal through entropic interactions between polymers and filamentous Pf bacteriophages, which are long, negatively charged filaments. This liquid crystalline structure enhances biofilm function by increasing adhesion and tolerance to desiccation and antibiotics. Pf bacteriophages are prevalent amongst P. aeruginosa clinical isolates and were detected in CF sputum. The addition of Pf bacteriophage to sputum polymers or serum was sufficient to drive their rapid assembly into viscous liquid crystals. Fd, a related bacteriophage of Escherichia coli, has similar biofilm-building capabilities. Targeting filamentous bacteriophage or the liquid crystalline organization of the biofilm matrix may represent antibacterial strategies.
doi:10.1016/j.chom.2015.10.013
PMCID: PMC4653043  PMID: 26567508
21.  Individual members of the microbiota disproportionately modulate host innate immune responses 
Cell host & microbe  2015;18(5):613-620.
Summary
Predicting host health status based on microbial community structure is a major goal of microbiome research. An implicit assumption of microbiome profiling for diagnostic purposes is that the proportional representation of different taxa determine host phenotypes. To test this assumption, we colonized gnotobiotic zebrafish with zebrafish-derived bacterial isolates and measured bacterial abundance and host neutrophil responses. Surprisingly, combinations of bacteria elicited immune responses that do not reflect the numerically dominant species. These data are consistent with a quantitative model in which the host responses to commensal species are additive, but where various species have different per capita immunostimulatory effects. For example, one species has a high per capita immunosuppression that is mediated through a potent secreted factor. We conclude that the proportional representation of bacteria in a community does not necessarily predict its functional capacities; however, characterizing specific properties of individual species offers predictive insights into multi-species community function.
doi:10.1016/j.chom.2015.10.009
PMCID: PMC4701053  PMID: 26567512
22.  M. tuberculosis T cell epitope analysis reveals paucity of antigenic variation and identifies rare variable TB antigens 
Cell host & microbe  2015;18(5):538-548.
Summary
Pathogens that evade adaptive immunity typically exhibit antigenic variation. By contrast, it appears that although the chronic human tuberculosis (TB)-causing pathogen Mycobacterium tuberculosis needs to counter host T cell responses, its T cell epitopes are hyperconserved. Here we present an extensive analysis of the T cell epitopes of M. tuberculosis. We combined population genomics with experimental immunology to determine the number and identity of T cell epitope sequence variants in 216 phylogenetically diverse strains of M. tuberculosis. Antigen conservation is indeed a hallmark M. tuberculosis. However, our analysis revealed a set of 7 variable antigens that were immunogenic in subjects with active TB. These findings suggest that M. tuberculosis uses mechanisms other than antigenic variation to evade T cells. T cell epitopes that exhibit sequence variation may not be subject to the same evasion mechanisms and hence vaccines that include such variable epitopes may be more efficacious.
doi:10.1016/j.chom.2015.10.008
PMCID: PMC4758912  PMID: 26607161
23.  The Ubiquitin Proteome of Toxoplasma gondii Reveals Roles for Protein Ubiquitination in Cell Cycle Transitions 
Cell host & microbe  2015;18(5):621-633.
Protein ubiquitination plays key roles in protein turnover, cellular signalling, and intracellular transport. The genome of Toxoplasma gondii encodes ubiquitination machinery but the roles of this posttranslational modification (PTM) are unknown. To examine the prevalence and function of ubiquitination in T. gondii, we mapped the ubiquitin proteome of tachyzoites. Over 500 ubiquitin-modified proteins, with almost 1000 sites, were identified on proteins with diverse localisations and functions. Enrichment analysis demonstrated that 35% of ubiquitinated proteins are cell cycle-regulated. Unexpectedly, most classic cell cycle regulators conserved in T. gondii were not detected in the ubiquitinome. Furthermore, many ubiquitinated proteins localise to the cytoskeleton and inner membrane complex, a structure beneath the plasma membrane facilitating division and host invasion. Comparing the ubiquitinome with other PTM proteomes reveals waves of PTM enrichment during the cell cycle. Thus, T. gondii PTMs are implicated as critical regulators of cell division and cell cycle transitions.
Graphical abstract
doi:10.1016/j.chom.2015.10.014
PMCID: PMC4968887  PMID: 26567513
Toxoplasma gondii; Ubiquitin; Apicomplexa; Parasite; Cell cycle; Posttranslational modification
24.  S. epidermidis Influence on Host Immunity: More Than Skin Deep 
Cell host & microbe  2015;17(2):143-144.
The mammalian immune system communicates with skin-resident microbes, and some of these microbes provide benefits to the host. In a recent paper in Nature, Naik et al. (2015) provide evidence that the murine epidermis permits S. epidermidis, a skin-specific bacterium, to shape the immune response.
doi:10.1016/j.chom.2015.01.012
PMCID: PMC5103695  PMID: 25674978
25.  The Salmonella Effector SteD Mediates MARCH8-Dependent Ubiquitination of MHC II Molecules and Inhibits T Cell Activation 
Cell Host & Microbe  2016;20(5):584-595.
Summary
The SPI-2 type III secretion system (T3SS) of intracellular Salmonella enterica translocates effector proteins into mammalian cells. Infection of antigen-presenting cells results in SPI-2 T3SS-dependent ubiquitination and reduction of surface-localized mature MHC class II (mMHCII). We identify the effector SteD as required and sufficient for this process. In Mel Juso cells, SteD localized to the Golgi network and vesicles containing the E3 ubiquitin ligase MARCH8 and mMHCII. SteD caused MARCH8-dependent ubiquitination and depletion of surface mMHCII. One of two transmembrane domains and the C-terminal cytoplasmic region of SteD mediated binding to MARCH8 and mMHCII, respectively. Infection of dendritic cells resulted in SteD-dependent depletion of surface MHCII, the co-stimulatory molecule B7.2, and suppression of T cell activation. SteD also accounted for suppression of T cell activation during Salmonella infection of mice. We propose that SteD is an adaptor, forcing inappropriate ubiquitination of mMHCII by MARCH8 and thereby suppressing T cell activation.
Graphical Abstract
Highlights
•Salmonella effector SteD promotes ubiquitination and surface depletion of mature MHCII•SteD binds both MHCII and the host E3 ubiquitin ligase MARCH8•SteD uses MARCH8 to ubiquitinate and surface deplete MHCII•SteD suppresses T cell activation during Salmonella infection in vitro and in mice
Dendritic cell infection by Salmonella depletes mature MHC class II (mMHCII) from the cell surface. Bayer-Santos et al. reveal that the Salmonella effector SteD binds the E3 ligase MARCH8 and mMHCII to promote mMHCII ubiquitination and surface depletion. SteD suppressed dendritic cell-mediated T cell activation in vitro and in mice.
doi:10.1016/j.chom.2016.10.007
PMCID: PMC5104694  PMID: 27832589
major histocompatibility complex; dendritic cells; Salmonella; effector; ubiquitin; ligase

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