PLOS Pathogens

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ISSN / EISSN : 15537366 / 15537374
Current Publisher: Public Library of Science (PLoS) (10.1371)
Total articles ≅ 7,695
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Michi Miura, Supravat Dey, Saumya Ramanayake, Abhyudai Singh, David S. Rueda, Charles R. M. Bangham
Published: 18 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008164

Abstract:The human T cell leukemia virus HTLV-1 establishes a persistent infection in vivo in which the viral sense-strand transcription is usually silent at a given time in each cell. However, cellular stress responses trigger the reactivation of HTLV-1, enabling the virus to transmit to a new host cell. Using single-molecule RNA FISH, we measured the kinetics of the HTLV-1 transcriptional reactivation in peripheral blood mononuclear cells (PBMCs) isolated from HTLV-1+ individuals. The abundance of the HTLV-1 sense and antisense transcripts was quantified hourly during incubation of the HTLV-1-infected PBMCs ex vivo. We found that, in each cell, the sense-strand transcription occurs in two distinct phases: the initial low-rate transcription is followed by a phase of rapid transcription. The onset of transcription peaked between 1 and 3 hours after the start of in vitro incubation. The variance in the transcription intensity was similar in polyclonal HTLV-1+ PBMCs (with tens of thousands of distinct provirus insertion sites), and in samples with a single dominant HTLV-1+ clone. A stochastic simulation model was developed to estimate the parameters of HTLV-1 proviral transcription kinetics. In PBMCs from a leukemic subject with one dominant T-cell clone, the model indicated that the average duration of HTLV-1 sense-strand activation by Tax (i.e. the rapid transcription) was less than one hour. HTLV-1 antisense transcription was stable during reactivation of the sense-strand. The antisense transcript HBZ was produced at an average rate of ~0.1 molecules per hour per HTLV-1+ cell; however, between 20% and 70% of HTLV-1-infected cells were HBZ-negative at a given time, the percentage depending on the individual subject. HTLV-1-infected cells are exposed to a range of stresses when they are drawn from the host, which initiate the viral reactivation. We conclude that whereas antisense-strand transcription is stable throughout the stress response, the HTLV-1 sense-strand reactivation is highly heterogeneous and occurs in short, self-terminating bursts. Human retroviruses such as HIV-1 and HTLV-1 (human T cell leukemia virus) can establish a latent infection in the host cell. However, these viruses need to be able to produce viral genome to propagate in a new host. HTLV-1-infected cells are transmitted through breastfeeding, blood transfusion and sexual contact, and HTLV-1 restores transcription once the infected cells are drawn from infected individuals. We measured the kinetics of the HTLV-1 transcriptional reactivation in blood cells isolated from HTLV-1+ individuals by single-molecule RNA FISH. Viral transcripts were visualized as diffraction-limited spots and their abundance was quantified at one-hour intervals. The onset of the virus transcription peaked after one to three hours of incubation. In each cell, a short period of slow HTLV-1 transcription was followed by a phase of rapid transcription. Computer simulation, based on experimental data on...
Ana Carreras-González, Diego Barriales, Ainhoa Palacios, Marta Montesinos-Robledo, Nicolás Navasa, Mikel Azkargorta, Ainize Peña-Cearra, Julen Tomás-Cortázar, Iraide Escobes, Miguel Angel Pascual-Itoiz, et al.
Published: 18 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008163

Abstract:Macrophages mediate the elimination of pathogens by phagocytosis resulting in the activation of specific signaling pathways that lead to the production of cytokines, chemokines and other factors. Borrelia burgdorferi, the causative agent of Lyme disease, causes a wide variety of pro-inflammatory symptoms. The proinflammatory capacity of macrophages is intimately related to the internalization of the spirochete. However, most receptors mediating this process are largely unknown. We have applied a multiomic approach, including the proteomic analysis of B. burgdorferi-containing phagosome-enriched fractions, to identify surface receptors that are involved in the phagocytic capacity of macrophages as well as their inflammatory output. Sucrose gradient protein fractions of human monocyte-derived macrophages exposed to B. burgdorferi contained the phagocytic receptor, CR3/CD14 highlighting the major role played by these proteins in spirochetal phagocytosis. Other proteins identified in these fractions include C-type lectins, scavenger receptors or Siglecs, of which some are directly involved in the interaction with the spirochete. We also identified the Fc gamma receptor pathway, including the binding receptor, CD64, as involved both in the phagocytosis of, and TNF induction in response to B. burgdorferi in the absence of antibodies. The common gamma chain, FcγR, mediates the phagocytosis of the spirochete, likely through Fc receptors and C-type lectins, in a process that involves Syk activation. Overall, these findings highlight the complex array of receptors involved in the phagocytic response of macrophages to B. burgdorferi. Macrophages eliminate infecting microorganisms through the concerted action of surface receptors and signaling molecules. As a consequence, these cells produce a series of soluble factors that participate in the inflammatory response during infections. The composition of the full complement of receptors that participate in the recognition and internalization of the causative agent of Lyme disease, Borrelia burgdorferi, is largely unknown. We have analyzed the protein composition of phagosomes containing B. burgdorferi from human macrophages and identified a series of surface proteins that may be involved in the process. Through the use of gene silencing techniques, we have determined the participation of several of these receptors both in the internalization of the bacterium and the subsequent inflammatory response. Among these, we have identified the Fc gamma receptor pathway as involved in this process in the absence of antibodies. We have also identified receptors that are directly involved in the attachment of B. burgdorferi, while others seem to have an accessory role in the internalization and/or induction of proinflammatory cytokines in response to the spirochete. These data clarify the complex array of interactions between macrophages and B. burgdorferi and shed light on the overall response to this infectious agent.
Peng Gao, Yue Chai, Jiangwei Song, Teng Liu, Peng Chen, Lei Zhou, Xinna Ge, Xin Guo, Jun Han, Hanchun Yang
Published: 18 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008169

Abstract:The unfolded protein response (UPR) in the endoplasmic reticulum (ER) constitutes a critical component of host innate immunity against microbial infections. In this report, we show that porcine reproductive and respiratory syndrome virus (PRRSV) utilizes the UPR machinery for its own benefit. We provide evidence that the virus targets the UPR central regulator GRP78 for proteasomal degradation via a mechanism that requires viral glycoprotein GP2a, while both IRE1-XBP1s and PERK-eIF2α-ATF4 signaling branches of the UPR are turned on at early stage of infection. The activated effector XBP1s was found to enter the nucleus, but ATF4 was unexpectedly diverted to cytoplasmic viral replication complexes by means of nonstructural proteins nsp2/3 to promote viral RNA synthesis. RNAi knockdown of either ATF4 or XBP1s dramatically attenuated virus titers, while overexpression caused increases. These observations reveal attractive host targets (e.g., ATF4 and XBP1s) for antiviral drugs and have implications in vaccine development. Porcine reproductive and respiratory syndrome virus (PRRSV) poses a major threat to the worldwide swine industry, but no effective vaccines or antiviral drugs are available. A better understanding of the pathogen-host interactions that support PRRSV replication is essential for understanding viral pathogenesis and the development of preventive measures. Here we report that PRRSV utilizes unconventional strategies to reprogram the unfolded protein response (UPR) of the host to its own advantage. The virus targets GRP78 for partial degradation to create a favorable environment for UPR induction and hijacks ATF4 into cytoplasmic replication complexes to promote viral RNA synthesis. The data also reveal potential targets (e.g., ATF4 and XBP1s) for antiviral drugs and have implications in vaccine development.
Kathryn A. Coe, WonSik Lee, Madeleine C. Stone, Gloria Komazin-Meredith, Timothy C. Meredith, Yonatan H. Grad, Suzanne Walker
Published: 18 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1007862

Abstract:Antibiotic-resistant Staphylococcus aureus remains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across the S. aureus phylogeny. Here we report the first direct comparison of multiple strains of S. aureus via transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. We treated the libraries with daptomycin to assess whether the strain-dependent differences impact pathways important for survival. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, consistently promote survival under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains. Antibiotic-resistant Staphylococcus aureus kills thousands of people every year in the United States alone. To stay ahead of the looming threat of multidrug-resistant infections, we must continue to develop new antibiotics and find ways to make our current repertoire of antibiotics more effective, including by finding pairs of compounds that perform best when administered together. In the age of next-generation sequencing, we can now use transposon sequencing to find potential targets for new antibiotics on a genome-wide scale, identified as either essential genes or genes that positively influence survival in the presence of an antibiotic. In this work, we created a compendium of genes that are essential across a range of S. aureus strains, as well as those that are important for growth in the presence of the antibiotic daptomycin. The results will be a resource for researchers working to develop the next generation of antibiotic therapies.
Haifeng Zhang, Wei Tang, Kaiyue Liu, Qian Huang, Xin Zhang, Xia Yan, Yue Chen, Jiansheng Wang, Zhongqiang Qi, Zhengyi Wang, et al.
Published: 15 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008187

Maya Glover, Stefano A. P. Colombo, David J. Thornton, Richard K. Grencis
Published: 15 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1007926

Abstract:The majority of experiments investigating the immune response to gastrointestinal helminth infection use a single bolus infection. However, in situ individuals are repeatedly infected with low doses. Therefore, to model natural infection, mice were repeatedly infected (trickle infection) with low doses of Trichuris muris. Trickle infection resulted in the slow acquisition of immunity reflected by a gradual increase in worm burden followed by partial expulsion. Flow cytometry revealed that the CD4+ T cell response shifted from Th1 dominated to Th2 dominated, which coincided with an increase in Type 2 cytokines. The development of resistance following trickle infection was associated with increased worm expulsion effector mechanisms including goblet cell hyperplasia, Muc5ac production and increased epithelial cell turn over. Depletion of CD4+ T cells reversed resistance confirming their importance in protective immunity following trickle infection. In contrast, depletion of group 2 innate lymphoid cells did not alter protective immunity. T. muris trickle infection resulted in a dysbiotic mircrobiota which began to recover alpha diversity following the development of resistance. These data establish trickle infection as a robust and informative model for analysis of immunity to chronic intestinal helminth infection more akin to that observed under natural infection conditions and confirms the importance of CD4+ T cell adaptive immunity in host protection. Infection with parasitic worms (helminths) is a considerable cause of morbidity in humans. Understanding how we respond to infection is crucial to developing novel therapies. Laboratory models of helminth infection have been a valuable tool in understanding fundamental immune responses to infection. However, typically an individual mouse will be infected with a large, single-dose of the parasite. This is in contrast to the natural scenario in which individuals will receive frequent low level exposures. However, it is unknown is how repeated infection alters the development of immunity to infection. We have developed a laboratory model to tackle this question. We infected mice with the model helminth Trichuris muris on a weekly basis and assessed a range of responses in comparison with a more traditional infection regime. We found striking differences in the dynamics of the infection, the host immune response, and in changes to host gut microbial populations. Our study shows how resistance to helminth infection can develop over time in response to repeat infection, and provides a model system that better reflects human immunity to this parasite.
Zhen Luo, Rui Su, Wenbiao Wang, Yicong Liang, Xiaofeng Zeng, Muhammad Adnan Shereen, Nadia Bashir, Qi Zhang, Ling Zhao, Kailang Wu, et al.
Published: 15 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008142

Abstract:As a neurotropic virus, human Enterovirus 71 (EV71) infection causes hand-foot-and-mouth disease (HFMD) and may develop severe neurological disorders in infants. Toll-like receptor 7 (TLR7) acts as an innate immune receptor and is also a death receptor in the central nervous system (CNS). However, the mechanisms underlying the regulation of TLR7-mediated brain pathogenesis upon EV71 infection remain largely elusive. Here we reveal a novel mechanism by which EV71 infects astrocytes in the brain and induces neural pathogenesis via TLR7 and interleukin-6 (IL-6) in C57BL/6 mice and in human astroglioma U251 cells. Upon EV71 infection, wild-type (WT) mice displayed more significant body weight loss, higher clinical scores, and lower survival rates as compared with TLR7-/- mice. In the cerebral cortex of EV71-infected mice, neurofilament integrity was disrupted, and inflammatory cell infiltration and neurodegeneration were induced in WT mice, whereas these were largely absent in TLR7-/- mice. Similarly, IL-6 production, Caspase-3 cleavage, and cell apoptosis were significantly higher in EV71-infected WT mice as compared with TLR7-/- mice. Moreover, EV71 preferentially infected and induced IL-6 in astrocytes of mice brain. In U251 cells, EV71-induced IL-6 production and cell apoptosis were suppressed by shRNA-mediated knockdown of TLR7 (shTLR7). Moreover, in the cerebral cortex of EV71-infected mice, the blockade of IL-6 with anti-IL-6 antibody (IL-6-Ab) restored the body weight loss, attenuated clinical scores, improved survival rates, reduced the disruption of neurofilament integrity, decreased cell apoptotic induction, and lowered levels of Caspase-3 cleavage. Similarly, in EV71-infected U251 cells, IL-6-Ab blocked EV71-induced IL-6 production and cell apoptosis in response to viral infection. Collectively, it’s exhibited TLR7 upregulation, IL-6 induction and astrocytic cell apoptosis in EV71-infected human brain. Taken together, we propose that EV71 infects astrocytes of the cerebral cortex in mice and human and triggers TLR7 signaling and IL-6 release, subsequently inducing neural pathogenesis in the brain. Enterovirus 71 (EV71) infection causes aseptic meningitis, poliomyelitis-like paralysis and fatal encephalitis in infants. Besides an immune receptor, toll-like receptor 7 (TLR7) serves as a death receptor in central nervous system (CNS). However, the role of TLR7 in EV71-induced neural pathogenesis remains ambiguous. This study reveals a distinct mechanism by which EV71 induces neurodegeneration via TLR7 and interleukin-6 (IL-6). Upon EV71 infection, TLR7-/- mice displayed less body weight loss, lower clinical score, and higher survival rate as compared with wild-type (WT) mice. Meanwhile, a severer histopathologic neurofilaments disruption, neurodegeneration and cell apoptosis were observed in brain of EV71-infected WT mice. IL-6 release, cell apoptosis, and Caspase-3 cleavage were attenuated by shRNA targeting TLR7 (shTLR7) in...
Han Kang Tee, Chee Wah Tan, Thinesshwary Yogarajah, Michelle Hui Pheng Lee, Hann Juang Chai, Nur Aziah Hanapi, Siti R. Yusof, Kien Chai Ong, Vannajan Sanghiran Lee, I-Ching Sam, et al.
Published: 15 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1007863

Abstract:Enterovirus A71 (EV-A71) causes hand, foot and mouth disease epidemics with neurological complications and fatalities. However, the neuropathogenesis of EV-A71 remains poorly understood. In mice, adaptation and virulence determinants have been mapped to mutations at VP2-149, VP1-145 and VP1-244. We investigate how these amino acids alter heparin-binding phenotype and shapes EV-A71 virulence in one-day old mice. We constructed six viruses with varying residues at VP1-98, VP1-145 (which are both heparin-binding determinants) and VP2-149 (based on the wild type 149K/98E/145Q, termed KEQ) to generate KKQ, KKE, KEE, IEE and IEQ variants. We demonstrated that the weak heparin-binder IEE was highly lethal in mice. The initially strong heparin-binding IEQ variant acquired an additional mutation VP1-K244E, which confers weak heparin-binding phenotype resulting in elevated viremia and increased brain virus antigens in mice, with subsequent high virulence. IEE and IEQ-244E variants inoculated into mice disseminated efficiently and displayed high viremia. Increasing polymerase fidelity and impairing recombination of IEQ attenuated the virulence, suggesting the importance of population diversity in EV-A71 pathogenesis in vivo. Combining in silico docking and deep sequencing approaches, we inferred that virus population diversity is shaped by electrostatic interactions at the five-fold axis of the virus surface. Electrostatic surface charges facilitate virus adaptation by generating poor heparin-binding variants for better in vivo dissemination in mice, likely due to reduced adsorption to heparin-rich peripheral tissues, which ultimately results in increased neurovirulence. The dynamic switching between heparin-binding and weak heparin-binding phenotype in vivo explained the neurovirulence of EV-A71. Enterovirus A71 (EV-A71) is the primary cause of hand, foot and mouth disease, and it can also infect the central nervous system and cause fatal outbreaks in young children. EV-A71 pathogenesis remains elusive. In this study, we demonstrated that EV-A71 variants with strong affinity to heparan sulfate (heparin) have a growth advantage in cell culture, but are disadvantaged in vivo. When inoculated into one-day old mice, strong heparin-binding virus variants are more likely to be adsorbed to peripheral tissues, resulting in impaired ability to disseminate, and are cleared from the bloodstream rapidly. The lower viremia level resulted in no neuroinvasion. In contrast, weak heparin-binding variants show greater levels of viremia, dissemination and subsequent neurovirulence in mice. We also provide evidence that the EV-A71 heparin-binding pattern is mediated by electrostatic surface charges on the virus capsid surface. In mice, EV-A71 undergoes adaptive mutation to acquire greater negative surface charges, thus generating new virulent variants with weak heparin-binding ability which allows greater viral spread. Our study underlines the importance of electrostatic...
Alfred T. Harding, Griffin D. Haas, Benjamin S. Chambers, Nicholas S. Heaton
Published: 15 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008098

Abstract:Influenza A viruses (IAVs) encode their genome across eight, negative sense RNA segments. During viral assembly, the failure to package all eight segments, or packaging a mutated segment, renders the resulting virion incompletely infectious. It is known that the accumulation of these defective particles can limit viral disease by interfering with the spread of fully infectious particles. In order to harness this phenomenon therapeutically, we defined which viral packaging signals were amenable to duplication and developed a viral genetic platform which produced replication competent IAVs that require up to two additional artificial genome segments for full infectivity. The modified and artificial genome segments propagated by this approach are capable of acting as “decoy” segments that, when packaged by coinfecting wild-type viruses, lead to the production of non-infectious viral particles. Although IAVs which require 10 genomic segments for full infectivity are able to replicate themselves and spread in vivo, their genomic modifications render them avirulent in mice. Administration of these viruses, both prophylactically and therapeutically, was able to rescue animals from a lethal influenza virus challenge. Together, our results show that replicating IAVs designed to propagate and spread defective genomic segments represent a potent anti-influenza biological therapy that can target the conserved process of particle assembly to limit viral disease. Influenza infections are best prevented via prophylactic vaccination. Vaccination, however, is incompletely efficacious, necessitating the use of anti-influenza therapeutics. To date, several different classes of anti-influenza therapeutics have been developed and used in order to combat these infections. Unfortunately, the incidence of influenza resistance to many of these therapeutics has begun to rise, necessitating the development of new strategies. One such strategy is to mimic the activity of naturally occurring viral particles that harbor defective genomes. These defective interfering particles have the ability to interfere with productive viral assembly, preventing the spread of influenza viruses across the respiratory tract. Furthermore, given the manner in which they target influenza segment packaging, a conserved feature of all influenza A viruses, resistance to this therapeutic strategy is unlikely. Here, we report the development of a genetic platform that allows the production of replicating influenza viruses which require 10 genomic segments to be fully infectious. These viruses are capable of amplifying themselves in isolation, but coinfection with a wild-type virus leads to segment exchange and compromises the spread of both viruses. This interference, while mechanistically distinct from naturally occurring defective particles, was able to target the same viral process and rescue animals exposed to an otherwise lethal viral infection. This viral-based approach may represent a...
Jason Buehler, Ethan Carpenter, Sebastian Zeltzer, Suzu Igarashi, Michael Rak, Iliyana Mikell, Jay A. Nelson, Felicia Goodrum
Published: 14 November 2019
PLOS Pathogens, Volume 15; doi:10.1371/journal.ppat.1008037

Abstract:Sustained phosphotinositide3-kinase (PI3K) signaling is critical to the maintenance of alpha and beta herpesvirus latency. We have previously shown that the beta-herpesvirus, human cytomegalovirus (CMV), regulates epidermal growth factor receptor (EGFR), upstream of PI3K, to control states of latency and reactivation. How signaling downstream of EGFR is regulated and how this impacts CMV infection and latency is not fully understood. We demonstrate that CMV downregulates EGFR early in the productive infection, which blunts the activation of EGFR and its downstream pathways in response to stimuli. However, CMV infection sustains basal levels of EGFR and downstream pathway activity in the context of latency in CD34+ hematopoietic progenitor cells (HPCs). Inhibition of MEK/ERK, STAT or PI3K/AKT pathways downstream of EGFR increases viral reactivation from latently infected CD34+ HPCs, defining a role for these pathways in latency. We hypothesized that CMV modulation of EGFR signaling might impact viral transcription important to latency. Indeed, EGF-stimulation increased expression of the UL138 latency gene, but not immediate early or early viral genes, suggesting that EGFR signaling promotes latent gene expression. The early growth response-1 (EGR1) transcription factor is induced downstream of EGFR signaling through the MEK/ERK pathway and is important for the maintenance of hematopoietic stemness. We demonstrate that EGR1 binds the viral genome upstream of UL138 and is sufficient to promote UL138 expression. Further, disruption of EGR1 binding upstream of UL138 prevents the establishment of latency in CD34+ HPCs. Our results indicate a model whereby UL138 modulation of EGFR signaling feeds back to promote UL138 gene expression and suppression of replication for latency. By this mechanism, the virus has hardwired itself into host cell biology to sense and respond to changes in homeostatic host cell signaling. Host signaling is important for regulating states of cytomegalovirus (CMV) replication and latency. We have shown that human cytomegalovirus regulates EGFR levels and trafficking and that sustained EGFR or downstream PI3K signaling is a requirement for viral latency. Changes in host signaling have the ability to alter viral and host gene expression to impact the outcome of infection. Here we show that EGFR signaling through MEK/ERK pathway induces the host EGR1 transcription factor that is highly expressed in hematopoietic stem cells and necessary for the maintenance of hematopoietic stemness. Downregulation of EGR1 promotes stem cell mobilization and differentiation, known stimuli for CMV reactivation. We identified functional EGR1 binding sites upstream of the UL138 CMV latency gene and EGR1 stimulated UL138 expression to reinforce the latent infection. Mutant viruses where the regulation of UL138 by EGR1 is disrupted are unable to establish latency in CD34+ HPCs. This study advances our understanding of how host signaling impacts...