PLOS Pathogens: New ArticlesPLOShttps://journals.plos.org/plospathogens/webmaster@plos.orghttps://journals.plos.org/plospathogens/feed/atomAll PLOS articles are Open Access.https://journals.plos.org/plospathogens/resource/img/favicon.icohttps://journals.plos.org/plospathogens/resource/img/favicon.ico2024-03-19T12:53:19ZBAG6 inhibits influenza A virus replication by inducing viral polymerase subunit PB2 degradation and perturbing RdRp complex assemblyYong ZhouTian LiYunfan ZhangNianzhi ZhangYuxin GuoXiaoyi GaoWenjing PengSicheng ShuChuankuo ZhaoDi CuiHonglei SunYipeng SunJinhua LiuJun TangRui ZhangJuan Pu10.1371/journal.ppat.10121102024-03-18T14:00:00Z2024-03-18T14:00:00Z<p>by Yong Zhou, Tian Li, Yunfan Zhang, Nianzhi Zhang, Yuxin Guo, Xiaoyi Gao, Wenjing Peng, Sicheng Shu, Chuankuo Zhao, Di Cui, Honglei Sun, Yipeng Sun, Jinhua Liu, Jun Tang, Rui Zhang, Juan Pu</p>
The interaction between influenza A virus (IAV) and host proteins is an important process that greatly influences viral replication and pathogenicity. PB2 protein is a subunit of viral ribonucleoprotein (vRNP) complex playing distinct roles in viral transcription and replication. BAG6 (BCL2-associated athanogene 6) as a multifunctional host protein participates in physiological and pathological processes. Here, we identify BAG6 as a new restriction factor for IAV replication through targeting PB2. For both avian and human influenza viruses, overexpression of BAG6 reduced viral protein expression and virus titers, whereas deletion of BAG6 significantly enhanced virus replication. Moreover, BAG6-knockdown mice developed more severe clinical symptoms and higher viral loads upon IAV infection. Mechanistically, BAG6 restricted IAV transcription and replication by inhibiting the activity of viral RNA-dependent RNA polymerase (RdRp). The co-Immunoprecipitation assays showed BAG6 specifically interacted with the N-terminus of PB2 and competed with PB1 for RdRp complex assembly. The ubiquitination assay indicated that BAG6 promoted PB2 ubiquitination at K189 residue and targeted PB2 for K48-linked ubiquitination degradation. The antiviral effect of BAG6 necessitated its N-terminal region containing a ubiquitin-like (UBL) domain (17-92aa) and a PB2-binding domain (124-186aa), which are synergistically responsible for viral polymerase subunit PB2 degradation and perturbing RdRp complex assembly. These findings unravel a novel antiviral mechanism via the interaction of viral PB2 and host protein BAG6 during avian or human influenza virus infection and highlight a potential application of BAG6 for antiviral drug development.Transposon sequencing reveals metabolic pathways essential for <i>Mycobacterium tuberculosis</i> infectionAlisha M. BlockParker C. WiegertSarah B. NamugenyiAnna D. Tischler10.1371/journal.ppat.10116632024-03-18T14:00:00Z2024-03-18T14:00:00Z<p>by Alisha M. Block, Parker C. Wiegert, Sarah B. Namugenyi, Anna D. Tischler</p>
New drugs are needed to shorten and simplify treatment of tuberculosis caused by <i>Mycobacterium tuberculosis</i>. Metabolic pathways that <i>M</i>. <i>tuberculosis</i> requires for growth or survival during infection represent potential targets for anti-tubercular drug development. Genes and metabolic pathways essential for <i>M</i>. <i>tuberculosis</i> growth in standard laboratory culture conditions have been defined by genome-wide genetic screens. However, whether <i>M</i>. <i>tuberculosis</i> requires these essential genes during infection has not been comprehensively explored because mutant strains cannot be generated using standard methods. Here we show that <i>M</i>. <i>tuberculosis</i> requires the phenylalanine (Phe) and <i>de novo</i> purine and thiamine biosynthetic pathways for mammalian infection. We used a defined collection of <i>M</i>. <i>tuberculosis</i> transposon (Tn) mutants in essential genes, which we generated using a custom nutrient-rich medium, and transposon sequencing (Tn-seq) to identify multiple central metabolic pathways required for fitness in a mouse infection model. We confirmed by individual retesting and complementation that mutations in <i>pheA</i> (Phe biosynthesis) or <i>purF</i> (purine and thiamine biosynthesis) cause death of <i>M</i>. <i>tuberculosis</i> in the absence of nutrient supplementation <i>in vitro</i> and strong attenuation in infected mice. Our findings show that Tn-seq with defined Tn mutant pools can be used to identify <i>M</i>. <i>tuberculosis</i> genes required during mouse lung infection. Our results also demonstrate that <i>M</i>. <i>tuberculosis</i> requires Phe and purine/thiamine biosynthesis for survival in the host, implicating these metabolic pathways as prime targets for the development of new antibiotics to combat tuberculosis.ALIX and TSG101 are essential for cellular entry and replication of two porcine alphacoronavirusesXiongnan ChenYifan LiangZhijun WengChen HuYunzhao PengYingshuo SunQi GaoZhao HuangShengqiu TangLang GongGuihong Zhang10.1371/journal.ppat.10121032024-03-15T14:00:00Z2024-03-15T14:00:00Z<p>by Xiongnan Chen, Yifan Liang, Zhijun Weng, Chen Hu, Yunzhao Peng, Yingshuo Sun, Qi Gao, Zhao Huang, Shengqiu Tang, Lang Gong, Guihong Zhang</p>
Alphacoronaviruses are the primary coronaviruses responsible for causing severe economic losses in the pig industry with the potential to cause human outbreaks. Currently, extensive studies have reported the essential role of endosomal sorting and transport complexes (ESCRT) in the life cycle of enveloped viruses. However, very little information is available about which ESCRT components are crucial for alphacoronaviruses infection. By using RNA interference in combination with Co-immunoprecipitation, as well as fluorescence and electron microscopy approaches, we have dissected the role of ALIX and TSG101 for two porcine alphacoronavirus cellular entry and replication. Results show that infection by two porcine alphacoronaviruses, including porcine epidemic diarrhea virus (PEDV) and porcine enteric alphacoronavirus (PEAV), is dramatically decreased in ALIX- or TSG101-depleted cells. Furthermore, PEDV entry significantly increases the interaction of ALIX with caveolin-1 (CAV1) and RAB7, which are crucial for viral endocytosis and lysosomal transport, however, does not require TSG101. Interestingly, PEAV not only relies on ALIX to regulate viral endocytosis and lysosomal transport, but also requires TSG101 to regulate macropinocytosis. Besides, ALIX and TSG101 are recruited to the replication sites of PEDV and PEAV where they become localized within the endoplasmic reticulum and virus-induced double-membrane vesicles. PEDV and PEAV replication were significantly inhibited by depletion of ALIX and TSG101 in Vero cells or primary jejunal epithelial cells, indicating that ALIX and TSG101 are crucial for PEDV and PEAV replication. Collectively, these data highlight the dual role of ALIX and TSG101 in the entry and replication of two porcine alphacoronaviruses. Thus, ESCRT proteins could serve as therapeutic targets against two porcine alphacoronaviruses infection.Renaming <i>Candida glabrata</i>—A case of taxonomic purity over clinical and public health pragmatismDavid W. Denning10.1371/journal.ppat.10120552024-03-15T14:00:00Z2024-03-15T14:00:00Z<p>by David W. Denning</p>Recent advances in the treatment of Ebola disease: A brief overviewL’Emir Wassim El AyoubiOmar MahmoudJohnny ZakhourSouha S. Kanj10.1371/journal.ppat.10120382024-03-15T14:00:00Z2024-03-15T14:00:00Z<p>by L’Emir Wassim El Ayoubi, Omar Mahmoud, Johnny Zakhour, Souha S. Kanj</p>
Ebola disease (EBOD) remains a significant and ongoing threat to African countries, characterized by a mortality rate of 25% to 90% in patients with high viral load and significant transmissibility. The most recent outbreak, reported in Uganda in September 2022, was declared officially over in January 2023. However, it was caused by the Sudan Ebola virus (SUDV), a culprit species not previously reported for a decade. Since its discovery in 1976, the management of EBOD has primarily relied on supportive care. Following the devastating outbreak in West Africa from 2014 to 2016 secondary to the Zaire Ebola virus (EBOV), where over 28,000 lives were lost, dedicated efforts to find effective therapeutic agents have resulted in considerable progress in treating and preventing disease secondary to EBOV. Notably, 2 monoclonal antibodies—Ebanga and a cocktail of monoclonal antibodies, called Inmazeb—received Food and Drug Administration (FDA) approval in 2020. Additionally, multiple vaccines have been approved for EBOD prevention by various regulatory bodies, with Ervebo, a recombinant vesicular stomatitis virus-vectored vaccine against EBOV being the first vaccine to receive approval by the FDA in 2019. This review covers the key signs and symptoms of EBOD, its modes of transmission, and the principles guiding supportive care. Furthermore, it explores recent advancements in treating and preventing EBOD, highlighting the unique properties of each therapeutic agent and the ongoing progress in discovering new treatments.Koch’s curse: How models of extreme pathology bias studies of host–pathogen interactionsKalyan K. DewanEric T. Harvill10.1371/journal.ppat.10119972024-03-15T14:00:00Z2024-03-15T14:00:00Z<p>by Kalyan K. Dewan, Eric T. Harvill</p>NIa-Pro of sugarcane mosaic virus targets Corn Cysteine Protease 1 (CCP1) to undermine salicylic acid-mediated defense in maizeWen YuanXi ChenKaitong DuTong JiangMengfei LiYanyong CaoXiangdong LiGunther DoehlemannZaifeng FanTao Zhou10.1371/journal.ppat.10120862024-03-14T14:00:00Z2024-03-14T14:00:00Z<p>by Wen Yuan, Xi Chen, Kaitong Du, Tong Jiang, Mengfei Li, Yanyong Cao, Xiangdong Li, Gunther Doehlemann, Zaifeng Fan, Tao Zhou</p>
Papain-like cysteine proteases (PLCPs) play pivotal roles in plant defense against pathogen invasions. While pathogens can secrete effectors to target and inhibit PLCP activities, the roles of PLCPs in plant-virus interactions and the mechanisms through which viruses neutralize PLCP activities remain largely uncharted. Here, we demonstrate that the expression and activity of a maize PLCP CCP1 (Corn Cysteine Protease), is upregulated following sugarcane mosaic virus (SCMV) infection. Transient silencing of CCP1 led to a reduction in PLCP activities, thereby promoting SCMV infection in maize. Furthermore, the knockdown of CCP1 resulted in diminished salicylic acid (SA) levels and suppressed expression of SA-responsive pathogenesis-related genes. This suggests that CCP1 plays a role in modulating the SA signaling pathway. Interestingly, NIa-Pro, the primary protease of SCMV, was found to interact with CCP1, subsequently inhibiting its protease activity. A specific motif within NIa-Pro termed the inhibitor motif was identified as essential for its interaction with CCP1 and the suppression of its activity. We have also discovered that the key amino acids responsible for the interaction between NIa-Pro and CCP1 are crucial for the virulence of SCMV. In conclusion, our findings offer compelling evidence that SCMV undermines maize defense mechanisms through the interaction of NIa-Pro with CCP1. Together, these findings shed a new light on the mechanism(s) controlling the arms races between virus and plant.Subversion of selective autophagy for the biogenesis of tombusvirus replication organelles inhibits autophagyYuanrong KangWenwu LinPeter D. Nagy10.1371/journal.ppat.10120852024-03-14T14:00:00Z2024-03-14T14:00:00Z<p>by Yuanrong Kang, Wenwu Lin, Peter D. Nagy</p>
Elaborate viral replication organelles (VROs) are formed to support positive-strand RNA virus replication in infected cells. VRO formation requires subversion of intracellular membranes by viral replication proteins. Here, we showed that the key ATG8f autophagy protein and NBR1 selective autophagy receptor were co-opted by Tomato bushy stunt virus (TBSV) and the closely-related carnation Italian ringspot virus. Knockdown of ATG8f or NBR1 in plants led to reduced tombusvirus replication, suggesting pro-viral function for selective autophagy. BiFC and proximity-labeling experiments showed that the TBSV p33 replication protein interacted with ATG8f and NBR1 to recruit them to VROs. In addition, we observed that several core autophagy proteins, such as ATG1a, ATG4, ATG5, ATG101 and the plant-specific SH3P2 autophagy adaptor proteins were also re-localized to TBSV VROs, suggesting that TBSV hijacks the autophagy machinery in plant cells. We demonstrated that subversion of autophagy components facilitated the recruitment of VPS34 PI3 kinase and enrichment of phospholipids, such as phosphatidylethanolamine and PI3P phosphoinositide in the VRO membranes. Hijacking of autophagy components into TBSV VROs led to inhibition of autophagic flux. We also found that a fraction of the subverted ATG8f and NBR1 was sequestered in biomolecular condensates associated with VROs. We propose that the VRO-associated condensates trap those autophagy proteins, taking them away from the autophagy pathway. Overall, tombusviruses hijack selective autophagy to provide phospholipid-rich membranes for replication and to regulate the antiviral autophagic flux.Uncovering a hidden functional role of the XRE-cupin protein PsdR as a novel quorum-sensing regulator in <i>Pseudomonas aeruginosa</i>Huifang QiuYuanhao LiMin YuanHuali ChenAjai A. DandekarWeijun Dai10.1371/journal.ppat.10120782024-03-14T14:00:00Z2024-03-14T14:00:00Z<p>by Huifang Qiu, Yuanhao Li, Min Yuan, Huali Chen, Ajai A. Dandekar, Weijun Dai</p>
XRE-cupin family proteins containing an DNA-binding domain and a cupin signal-sensing domain are widely distributed in bacteria. In <i>Pseudomonas aeruginosa</i>, XRE-cupin transcription factors have long been recognized as regulators exclusively controlling cellular metabolism pathways. However, their potential functional roles beyond metabolism regulation remain unknown. PsdR, a typical XRE-cupin transcriptional regulator, was previously characterized as a local repressor involved solely in dipeptide metabolism. Here, by measuring quorum-sensing (QS) activities and QS-controlled metabolites, we uncover that PsdR is a new QS regulator in <i>P</i>. <i>aeruginosa</i>. Our RNA-seq analysis showed that rather than a local regulator, PsdR controls a large regulon, including genes associated with both the QS circuit and non-QS pathways. To unveil the underlying mechanism of PsdR in modulating QS, we developed a comparative transcriptome approach named “transcriptome profile similarity analysis” (TPSA). Using this TPSA method, we revealed that PsdR expression causes a QS-null-like transcriptome profile, resulting in QS-inactive phenotypes. Based on the results of TPSA, we further demonstrate that PsdR directly binds to the promoter for the gene encoding the QS master transcription factor LasR, thereby negatively regulating its expression and influencing QS activation. Moreover, our results showed that PsdR functions as a negative virulence regulator, as inactivation of PsdR enhanced bacterial cytotoxicity on host cells. In conclusion, we report on a new QS regulation role for PsdR, providing insights into its role in manipulating QS-controlled virulence. Most importantly, our findings open the door for a further discovery of untapped functions for other XRE-Cupin family proteins.Chikungunya virus infection disrupts MHC-I antigen presentation via nonstructural protein 2Brian C. WareM. Guston ParksMariana O. L. da SilvaThomas E. Morrison10.1371/journal.ppat.10117942024-03-14T14:00:00Z2024-03-14T14:00:00Z<p>by Brian C. Ware, M. Guston Parks, Mariana O. L. da Silva, Thomas E. Morrison</p>
Infection by chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes severe polyarthralgia and polymyalgia, which can last in some people for months to years. Chronic CHIKV disease signs and symptoms are associated with the persistence of viral nucleic acid and antigen in tissues. Like humans and nonhuman primates, CHIKV infection in mice results in the development of robust adaptive antiviral immune responses. Despite this, joint tissue fibroblasts survive CHIKV infection and can support persistent viral replication, suggesting that they escape immune surveillance. Here, using a recombinant CHIKV strain encoding the fluorescent protein VENUS with an embedded CD8<sup>+</sup> T cell epitope, SIINFEKL, we observed a marked loss of both MHC class I (MHC-I) surface expression and antigen presentation by CHIKV-infected joint tissue fibroblasts. Both <i>in vivo</i> and <i>ex vivo</i> infected joint tissue fibroblasts displayed reduced cell surface levels of H2-K<sup>b</sup> and H2-D<sup>b</sup> MHC-I proteins while maintaining similar levels of other cell surface proteins. Mutations within the methyl transferase-like domain of the CHIKV nonstructural protein 2 (nsP2) increased MHC-I cell surface expression and antigen presentation efficiency by CHIKV-infected cells. Moreover, expression of WT nsP2 alone, but not nsP2 with mutations in the methyltransferase-like domain, resulted in decreased MHC-I antigen presentation efficiency. MHC-I surface expression and antigen presentation was rescued by replacing VENUS-SIINFEKL with SIINFEKL tethered to β2-microglobulin in the CHIKV genome, which bypasses the requirement for peptide processing and TAP-mediated peptide transport into the endoplasmic reticulum. Collectively, this work suggests that CHIKV escapes the surveillance of antiviral CD8<sup>+</sup> T cells, in part, by nsP2-mediated disruption of MHC-I antigen presentation.Loxapine inhibits replication of hepatitis A virus <i>in vitro</i> and <i>in vivo</i> by targeting viral protein 2CMami MatsudaAsuka Hirai-YukiOsamu KotaniMichiyo KataokaXin ZhengDaisuke YamaneMasaru YokoyamaKoji IshiiMasamichi MuramatsuRyosuke Suzuki10.1371/journal.ppat.10120912024-03-13T14:00:00Z2024-03-13T14:00:00Z<p>by Mami Matsuda, Asuka Hirai-Yuki, Osamu Kotani, Michiyo Kataoka, Xin Zheng, Daisuke Yamane, Masaru Yokoyama, Koji Ishii, Masamichi Muramatsu, Ryosuke Suzuki</p>
No antiviral drugs currently are available for treatment of infection by hepatitis A virus (HAV), a causative agent of acute hepatitis, a potentially life-threatening disease. Chemical screening of a small-compound library using nanoluciferase-expressing HAV identified loxapine succinate, a selective dopamine receptor D2 antagonist, as a potent inhibitor of HAV propagation <i>in vitro</i>. Loxapine succinate did not inhibit viral entry nor internal ribosome entry site (IRES)-dependent translation, but exhibited strong inhibition of viral RNA replication. Blind passage of HAV in the presence of loxapine succinate resulted in the accumulation of viruses containing mutations in the 2C-encoding region, which contributed to resistance to loxapine succinate. Analysis of molecular dynamics simulations of the interaction between 2C and loxapine suggested that loxapine binds to the N-terminal region of 2C, and that resistant mutations impede these interactions. We further demonstrated that administration of loxapine succinate to HAV-infected <i>Ifnar1</i><sup>-/-</sup> mice (which lack the type I interferon receptor) results in decreases in the levels of fecal HAV RNA and of intrahepatic HAV RNA at an early stage of infection. These findings suggest that HAV protein 2C is a potential target for antivirals, and provide novel insights into the development of drugs for the treatment of hepatitis A.KSHV vIL-6 promotes SIRT3-induced deacetylation of SERBP1 to inhibit ferroptosis and enhance cellular transformation by inducing lipoyltransferase 2 mRNA degradationJing ZhouTianjiao WangHaoran ZhangJianhong LiuPengjun WeiRuoqi XuQin YanGuochun ChenWan LiShou-Jiang GaoChun Lu10.1371/journal.ppat.10120822024-03-12T14:00:00Z2024-03-12T14:00:00Z<p>by Jing Zhou, Tianjiao Wang, Haoran Zhang, Jianhong Liu, Pengjun Wei, Ruoqi Xu, Qin Yan, Guochun Chen, Wan Li, Shou-Jiang Gao, Chun Lu</p>
Ferroptosis, a defensive strategy commonly employed by the host cells to restrict pathogenic infections, has been implicated in the development and therapeutic responses of various types of cancer. However, the role of ferroptosis in oncogenic Kaposi’s sarcoma-associated herpesvirus (KSHV)-induced cancers remains elusive. While a growing number of non-histone proteins have been identified as acetylation targets, the functions of these modifications have yet to be revealed. Here, we show KSHV reprogramming of host acetylation proteomics following cellular transformation of rat primary mesenchymal precursor. Among them, SERPINE1 mRNA binding protein 1 (SERBP1) deacetylation is increased and required for KSHV-induced cellular transformation. Mechanistically, KSHV-encoded viral interleukin-6 (vIL-6) promotes SIRT3 deacetylation of SERBP1, preventing its binding to and protection of lipoyltransferase 2 (Lipt2) mRNA from mRNA degradation resulting in ferroptosis. Consequently, a SIRT3-specific inhibitor, 3-TYP, suppresses KSHV-induced cellular transformation by inducing ferroptosis. Our findings unveil novel roles of vIL-6 and SERBP1 deacetylation in regulating ferroptosis and KSHV-induced cellular transformation, and establish the vIL-6-SIRT3-SERBP1-ferroptosis pathways as a potential new therapeutic target for KSHV-associated cancers.Hepatitis B virus e antigen induces atypical metabolism and differentially regulates programmed cell deaths of macrophagesYumei LiChristine WuJiyoung LeeQiqi NingJuhyeon LimHyungjin EohSean WangBenjamin P. HurrellOmid AkbariJing-hsiung James Ou10.1371/journal.ppat.10120792024-03-11T14:00:00Z2024-03-11T14:00:00Z<p>by Yumei Li, Christine Wu, Jiyoung Lee, Qiqi Ning, Juhyeon Lim, Hyungjin Eoh, Sean Wang, Benjamin P. Hurrell, Omid Akbari, Jing-hsiung James Ou</p>
Macrophages can undergo M1-like proinflammatory polarization with low oxidative phosphorylation (OXPHOS) and high glycolytic activities or M2-like anti-inflammatory polarization with the opposite metabolic activities. Here we show that M1-like macrophages induced by hepatitis B virus (HBV) display high OXPHOS and low glycolytic activities. This atypical metabolism induced by HBV attenuates the antiviral response of M1-like macrophages and is mediated by HBV e antigen (HBeAg), which induces death receptor 5 (DR5) via toll-like receptor 4 (TLR4) to induce death-associated protein 3 (DAP3). DAP3 then induces the expression of mitochondrial genes to promote OXPHOS. HBeAg also enhances the expression of glutaminases and increases the level of glutamate, which is converted to α-ketoglutarate, an important metabolic intermediate of the tricarboxylic acid cycle, to promote OXPHOS. The induction of DR5 by HBeAg leads to apoptosis of M1-like and M2-like macrophages, although HBeAg also induces pyroptosis of the former. These findings reveal novel activities of HBeAg, which can reprogram mitochondrial metabolism and trigger different programmed cell death responses of macrophages depending on their phenotypes to promote HBV persistence.<i>Candida auris</i> undergoes adhesin-dependent and -independent cellular aggregationChloe PelletierSophie ShawSakinah AlsayeghAlistair J. P. BrownAlexander Lorenz10.1371/journal.ppat.10120762024-03-11T14:00:00Z2024-03-11T14:00:00Z<p>by Chloe Pelletier, Sophie Shaw, Sakinah Alsayegh, Alistair J. P. Brown, Alexander Lorenz</p>
<i>Candida auris</i> is a fungal pathogen of humans responsible for nosocomial infections with high mortality rates. High levels of resistance to antifungal drugs and environmental persistence mean these infections are difficult to treat and eradicate from a healthcare setting. Understanding the life cycle and the genetics of this fungus underpinning clinically relevant traits, such as antifungal resistance and virulence, is of the utmost importance to develop novel treatments and therapies. Epidemiological and genomic studies have identified five geographical clades (I-V), which display phenotypic and genomic differences. Aggregation of cells, a phenotype primarily of clade III strains, has been linked to reduced virulence in some infection models. The aggregation phenotype has thus been associated with conferring an advantage for (skin) colonisation rather than for systemic infection. However, strains with different clade affiliations were compared to infer the effects of different morphologies on virulence. This makes it difficult to distinguish morphology-dependent causes from clade-specific or even strain-specific genetic factors. Here, we identify two different types of aggregation: one induced by antifungal treatment which is a result of a cell separation defect; and a second which is controlled by growth conditions and only occurs in strains with the ability to aggregate. The latter aggregation type depends on an ALS-family adhesin which is differentially expressed during aggregation in an aggregative <i>C</i>. <i>auris</i> strain. Finally, we demonstrate that macrophages cannot clear aggregates, suggesting that aggregation might after all provide a benefit during systemic infection and could facilitate long-term persistence in the host.Editorial Note: Bradykinin B<sub>2</sub> Receptors of Dendritic Cells, Acting as Sensors of Kinins Proteolytically Released by Trypanosoma cruzi, Are Critical for the Development of Protective Type-1 ResponsesThe PLOS Pathogens Editors10.1371/journal.ppat.10120702024-03-11T14:00:00Z2024-03-11T14:00:00Z<p>by The PLOS Pathogens Editors </p>Computationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohortsXinyu ZhangYing HuRal E. VandenhoudtChunhua YanVincent C. MarconiMardge H. CohenZuoheng WangAmy C. JusticeBradley E. AouizeratKe Xu10.1371/journal.ppat.10120632024-03-11T14:00:00Z2024-03-11T14:00:00Z<p>by Xinyu Zhang, Ying Hu, Ral E. Vandenhoudt, Chunhua Yan, Vincent C. Marconi, Mardge H. Cohen, Zuoheng Wang, Amy C. Justice, Bradley E. Aouizerat, Ke Xu</p>
Background <p>Epigenome-wide association studies (EWAS) have identified CpG sites associated with HIV infection in blood cells in bulk, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. In this study, we aim to identify differentially methylated CpG sites for HIV infection in immune cell types: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes.</p> Methods <p>Applying a computational deconvolution method, we performed a cell-type based EWAS for HIV infection in three independent cohorts (N<sub>total</sub> = 1,382). DNA methylation in blood or in peripheral blood mononuclear cells (PBMCs) was profiled by an array-based method and then deconvoluted by Tensor Composition Analysis (TCA). The TCA-computed CpG methylation in each cell type was first benchmarked by bisulfite DNA methylation capture sequencing in a subset of the samples. Cell-type EWAS of HIV infection was performed in each cohort separately and a meta-EWAS was conducted followed by gene set enrichment analysis.</p> Results <p>The meta-analysis unveiled a total of 2,021 cell-type unique significant CpG sites for five inferred cell types. Among these inferred cell-type unique CpG sites, the concordance rate in the three cohorts ranged from 96% to 100% in each cell type. Cell-type level meta-EWAS unveiled distinct patterns of HIV-associated differential CpG methylation, where 74% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of unique HIV-associated CpG sites (N = 1,624) compared to any other cell type. Genes harboring significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CD4+ T-cells: <i>NLRC5</i>, <i>CX3CR1</i>, B cells: <i>IFI44L</i>, NK cells: <i>IL12R</i>, monocytes: <i>IRF7</i>), and in oncogenesis (e.g. CD4+ T-cells: <i>BCL family</i>, <i>PRDM16</i>, monocytes: <i>PRDM16</i>, <i>PDCD1LG2</i>). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis that were enriched among interferon-α and -γ, TNF-α, inflammatory response, and apoptotic pathways.</p> Conclusion <p>Our findings uncovered computationally inferred cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding HIV pathogenesis.</p>Repeated sensitization of mice with microfilariae of <i>Litomosoides sigmodontis</i> induces pulmonary eosinophilia in an IL-33-dependent mannerBenjamin LenzAlexandra EhrensJesuthas AjendraFrederic RischJoséphine GalAnna-Lena NeumannJulia J. ReichwaldWiebke StrutzHenry J. McSorleyCoralie MartinAchim HoeraufMarc P. Hübner10.1371/journal.ppat.10120712024-03-08T14:00:00Z2024-03-08T14:00:00Z<p>by Benjamin Lenz, Alexandra Ehrens, Jesuthas Ajendra, Frederic Risch, Joséphine Gal, Anna-Lena Neumann, Julia J. Reichwald, Wiebke Strutz, Henry J. McSorley, Coralie Martin, Achim Hoerauf, Marc P. Hübner</p>
Background <p>Eosinophilia is a hallmark of helminth infections and eosinophils are essential in the protective immune responses against helminths. Nevertheless, the distinct role of eosinophils during parasitic filarial infection, allergy and autoimmune disease-driven pathology is still not sufficiently understood. In this study, we established a mouse model for microfilariae-induced eosinophilic lung disease (ELD), a manifestation caused by eosinophil hyper-responsiveness within the lung.</p> Methods <p>Wild-type (WT) BALB/c mice were sensitized with dead microfilariae (MF) of the rodent filarial nematode <i>Litomosoides sigmodontis</i> three times at weekly intervals and subsequently challenged with viable MF to induce ELD. The resulting immune response was compared to non-sensitized WT mice as well as sensitized eosinophil-deficient dblGATA mice using flow cytometry, lung histology and ELISA. Additionally, the impact of IL-33 signaling on ELD development was investigated using the IL-33 antagonist HpARI2.</p> Results <p>ELD-induced WT mice displayed an increased type 2 immune response in the lung with increased frequencies of eosinophils, alternatively activated macrophages and group 2 innate lymphoid cells, as well as higher peripheral blood IgE, IL-5 and IL-33 levels in comparison to mice challenged only with viable MF or PBS. ELD mice had an increased MF retention in lung tissue, which was in line with an enhanced MF clearance from peripheral blood. Using eosinophil-deficient dblGATA mice, we demonstrate that eosinophils are essentially involved in driving the type 2 immune response and retention of MF in the lung of ELD mice. Furthermore, we demonstrate that IL-33 drives eosinophil activation <i>in vitro</i> and inhibition of IL-33 signaling during ELD induction reduces pulmonary type 2 immune responses, eosinophil activation and alleviates lung lacunarity.In conclusion, we demonstrate that IL-33 signaling is essentially involved in MF-induced ELD development.</p> Summary <p>Our study demonstrates that repeated sensitization of BALB/c mice with <i>L</i>. <i>sigmodontis</i> MF induces pulmonary eosinophilia in an IL-33-dependent manner. The newly established model recapitulates the characteristic features known to occur during eosinophilic lung diseases (ELD) such as human tropical pulmonary eosinophilia (TPE), which includes the retention of microfilariae in the lung tissue and induction of pulmonary eosinophilia and type 2 immune responses. Our study provides compelling evidence that IL-33 drives eosinophil activation during ELD and that blocking IL-33 signaling using HpARI2 reduces eosinophil activation, eosinophil accumulation in the lung tissue, suppresses type 2 immune responses and mitigates the development of structural damage to the lung. Consequently, IL-33 is a potential therapeutic target to reduce eosinophil-mediated pulmonary pathology.</p>Modulation of nucleotide metabolism by picornavirusesLonneke V. NouwenMartijn BreeuwsmaEsther A. ZaalChris H. A. van de LestInge BuitendijkMarleen ZwaagstraPascal BalićDmitri V. FilippovCelia R. BerkersFrank J. M. van Kuppeveld10.1371/journal.ppat.10120362024-03-08T14:00:00Z2024-03-08T14:00:00Z<p>by Lonneke V. Nouwen, Martijn Breeuwsma, Esther A. Zaal, Chris H. A. van de Lest, Inge Buitendijk, Marleen Zwaagstra, Pascal Balić, Dmitri V. Filippov, Celia R. Berkers, Frank J. M. van Kuppeveld</p>
Viruses actively reprogram the metabolism of the host to ensure the availability of sufficient building blocks for virus replication and spreading. However, relatively little is known about how picornaviruses—a large family of small, non-enveloped positive-strand RNA viruses—modulate cellular metabolism for their own benefit. Here, we studied the modulation of host metabolism by coxsackievirus B3 (CVB3), a member of the enterovirus genus, and encephalomyocarditis virus (EMCV), a member of the cardiovirus genus, using steady-state as well as <sup>13</sup>C-glucose tracing metabolomics. We demonstrate that both CVB3 and EMCV increase the levels of pyrimidine and purine metabolites and provide evidence that this increase is mediated through degradation of nucleic acids and nucleotide recycling, rather than upregulation of <i>de novo</i> synthesis. Finally, by integrating our metabolomics data with a previously acquired phosphoproteomics dataset of CVB3-infected cells, we identify alterations in phosphorylation status of key enzymes involved in nucleotide metabolism, providing insight into the regulation of nucleotide metabolism during infection.Impact of interkingdom microbial interactions in the vaginal tractShirli CohenKyla S. OstKelly S. Doran10.1371/journal.ppat.10120182024-03-08T14:00:00Z2024-03-08T14:00:00Z<p>by Shirli Cohen, Kyla S. Ost, Kelly S. Doran</p>Small molecule mediators of host-<i>T</i>. <i>cruzi-</i>environment interactions in Chagas diseaseGodwin Kwakye-NuakoCaitlyn E. MiddletonLaura-Isobel McCall10.1371/journal.ppat.10120122024-03-08T14:00:00Z2024-03-08T14:00:00Z<p>by Godwin Kwakye-Nuako, Caitlyn E. Middleton, Laura-Isobel McCall</p>
Small molecules (less than 1,500 Da) include major biological signals that mediate host-pathogen-microbiome communication. They also include key intermediates of metabolism and critical cellular building blocks. Pathogens present with unique nutritional needs that restrict pathogen colonization or promote tissue damage. In parallel, parts of host metabolism are responsive to immune signaling and regulated by immune cascades. These interactions can trigger both adaptive and maladaptive metabolic changes in the host, with microbiome-derived signals also contributing to disease progression. In turn, targeting pathogen metabolic needs or maladaptive host metabolic changes is an important strategy to develop new treatments for infectious diseases. <i>Trypanosoma cruzi</i> is a single-celled eukaryotic pathogen and the causative agent of Chagas disease, a neglected tropical disease associated with cardiac and intestinal dysfunction. Here, we discuss the role of small molecules during <i>T</i>. <i>cruzi</i> infection in its vector and in the mammalian host. We integrate these findings to build a theoretical interpretation of how maladaptive metabolic changes drive Chagas disease and extrapolate on how these findings can guide drug development.Streptolysin S is required for <i>Streptococcus pyogenes</i> nasopharyngeal and skin infection in HLA-transgenic miceBlake A. ShannonJacklyn R. HurstRonald S. FlannaganHeather C. CraigAanchal RishiKatherine J. KasperStephen W. TuffsDavid E. HeinrichsJohn K. McCormick10.1371/journal.ppat.10120722024-03-07T14:00:00Z2024-03-07T14:00:00Z<p>by Blake A. Shannon, Jacklyn R. Hurst, Ronald S. Flannagan, Heather C. Craig, Aanchal Rishi, Katherine J. Kasper, Stephen W. Tuffs, David E. Heinrichs, John K. McCormick</p>
<i>Streptococcus pyogenes</i> is a human-specific pathogen that commonly colonizes the upper respiratory tract and skin, causing a wide variety of diseases ranging from pharyngitis to necrotizing fasciitis and toxic shock syndrome. <i>S</i>. <i>pyogenes</i> has a repertoire of secreted virulence factors that promote infection and evasion of the host immune system including the cytolysins streptolysin O (SLO) and streptolysin S (SLS). <i>S</i>. <i>pyogenes</i> does not naturally infect the upper respiratory tract of mice although mice transgenic for MHC class II human leukocyte antigens (HLA) become highly susceptible. Here we used HLA-transgenic mice to assess the role of both SLO and SLS during both nasopharyngeal and skin infection. Using <i>S</i>. <i>pyogenes</i> MGAS8232 as a model strain, we found that an SLS-deficient strain exhibited a 100-fold reduction in bacterial recovery from the nasopharynx and a 10-fold reduction in bacterial burden in the skin, whereas an SLO-deficient strain did not exhibit any infection defects in these models. Furthermore, depletion of neutrophils significantly restored the bacterial burden of the SLS-deficient bacteria in skin, but not in the nasopharynx. In mice nasally infected with the wildtype <i>S</i>. <i>pyogenes</i>, there was a marked change in localization of the tight junction protein ZO-1 at the site of infection, demonstrating damage to the nasal epithelia that was absent in mice infected with the SLS-deficient strain. Overall, we conclude that SLS is required for the establishment of nasopharyngeal infection and skin infection in HLA-transgenic mice by <i>S</i>. <i>pyogenes</i> MGAS8232 and provide evidence that SLS contributes to nasopharyngeal infection through the localized destruction of nasal epithelia.Multiple genetic loci influence vaccine-induced protection against <i>Mycobacterium tuberculosis</i> in genetically diverse miceSherry L. KurtzRichard E. BakerFrederick J. BoehmChelsea C. LehmanLara R. MitterederHamda KhanAmy P. RossiDaniel M. GattiGillian BeamerChristopher M. SassettiKaren L. Elkins10.1371/journal.ppat.10120692024-03-07T14:00:00Z2024-03-07T14:00:00Z<p>by Sherry L. Kurtz, Richard E. Baker, Frederick J. Boehm, Chelsea C. Lehman, Lara R. Mittereder, Hamda Khan, Amy P. Rossi, Daniel M. Gatti, Gillian Beamer, Christopher M. Sassetti, Karen L. Elkins</p>
<i>Mycobacterium tuberculosis</i> (M.tb.) infection leads to over 1.5 million deaths annually, despite widespread vaccination with BCG at birth. Causes for the ongoing tuberculosis endemic are complex and include the failure of BCG to protect many against progressive pulmonary disease. Host genetics is one of the known factors implicated in susceptibility to primary tuberculosis, but less is known about the role that host genetics plays in controlling host responses to vaccination against M.tb. Here, we addressed this gap by utilizing Diversity Outbred (DO) mice as a small animal model to query genetic drivers of vaccine-induced protection against M.tb. DO mice are a highly genetically and phenotypically diverse outbred population that is well suited for fine genetic mapping. Similar to outcomes in people, our previous studies demonstrated that DO mice have a wide range of disease outcomes following BCG vaccination and M.tb. challenge. In the current study, we used a large population of BCG-vaccinated/M.tb.-challenged mice to perform quantitative trait loci mapping of complex infection traits; these included lung and spleen M.tb. burdens, as well as lung cytokines measured at necropsy. We found sixteen chromosomal loci associated with complex infection traits and cytokine production. QTL associated with bacterial burdens included a region encoding major histocompatibility antigens that are known to affect susceptibility to tuberculosis, supporting validity of the approach. Most of the other QTL represent novel associations with immune responses to M.tb. and novel pathways of cytokine regulation. Most importantly, we discovered that protection induced by BCG is a multigenic trait, in which genetic loci harboring functionally-distinct candidate genes influence different aspects of immune responses that are crucial collectively for successful protection. These data provide exciting new avenues to explore and exploit in developing new vaccines against M.tb.Comparative analysis of human, rodent and snake deltavirus replicationPierre KhalfiZoé DenisJoe McKellarGiovanni MerollaCarine ChaveyJosé Ursic-BedoyaLena SoppaLeonora SziroviczaUdo HetzelJeremy DufourtCedric LeyratNora GoldmannKaku GotoEloi VerrierThomas F. BaumertDieter GlebeValérie CourgnaudDamien GregoireJussi HepojokiKarim Majzoub10.1371/journal.ppat.10120602024-03-05T14:00:00Z2024-03-05T14:00:00Z<p>by Pierre Khalfi, Zoé Denis, Joe McKellar, Giovanni Merolla, Carine Chavey, José Ursic-Bedoya, Lena Soppa, Leonora Szirovicza, Udo Hetzel, Jeremy Dufourt, Cedric Leyrat, Nora Goldmann, Kaku Goto, Eloi Verrier, Thomas F. Baumert, Dieter Glebe, Valérie Courgnaud, Damien Gregoire, Jussi Hepojoki, Karim Majzoub</p>
The recent discovery of Hepatitis D (HDV)<i>-like</i> viruses across a wide range of taxa led to the establishment of the <i>Kolmioviridae</i> family. Recent studies suggest that kolmiovirids can be satellites of viruses other than Hepatitis B virus (HBV), challenging the strict HBV/HDV-association dogma. Studying whether kolmiovirids are able to replicate in any animal cell they enter is essential to assess their zoonotic potential. Here, we compared replication of three kolmiovirids: HDV, rodent (RDeV) and snake (SDeV) deltavirus <i>in vitro</i> and <i>in vivo</i>. We show that SDeV has the narrowest and RDeV the broadest host cell range. High resolution imaging of cells persistently replicating these viruses revealed nuclear viral hubs with a peculiar RNA-protein organization. Finally, <i>in vivo</i> hydrodynamic delivery of viral replicons showed that both HDV and RDeV, but not SDeV, efficiently replicate in mouse liver, forming massive nuclear viral hubs. Our comparative analysis lays the foundation for the discovery of specific host factors controlling <i>Kolmioviridae</i> host-shifting.Rubisco small subunit (RbCS) is co-opted by potyvirids as the scaffold protein in assembling a complex for viral intercellular movementLi QinHongjun LiuPeilan LiuLu JiangXiaofei ChengFangfang LiWentao ShenWenping QiuZhaoji DaiHongguang Cui10.1371/journal.ppat.10120642024-03-04T14:00:00Z2024-03-04T14:00:00Z<p>by Li Qin, Hongjun Liu, Peilan Liu, Lu Jiang, Xiaofei Cheng, Fangfang Li, Wentao Shen, Wenping Qiu, Zhaoji Dai, Hongguang Cui</p>
Plant viruses must move through plasmodesmata (PD) to complete their life cycles. For viruses in the <i>Potyviridae</i> family (potyvirids), three viral factors (P3N-PIPO, CI, and CP) and few host proteins are known to participate in this event. Nevertheless, not all the proteins engaging in the cell-to-cell movement of potyvirids have been discovered. Here, we found that HCPro2 encoded by areca palm necrotic ring spot virus (ANRSV) assists viral intercellular movement, which could be functionally complemented by its counterpart HCPro from a potyvirus. Affinity purification and mass spectrometry identified several viral factors (including CI and CP) and host proteins that are physically associated with HCPro2. We demonstrated that HCPro2 interacts with both CI and CP <i>in planta</i> in forming PD-localized complexes during viral infection. Further, we screened HCPro2-associating host proteins, and identified a common host protein in <i>Nicotiana benthamiana</i>–Rubisco small subunit (NbRbCS) that mediates the interactions of HCPro2 with CI or CP, and CI with CP. Knockdown of <i>NbRbCS</i> impairs these interactions, and significantly attenuates the intercellular and systemic movement of ANRSV and three other potyvirids (turnip mosaic virus, pepper veinal mottle virus, and telosma mosaic virus). This study indicates that a nucleus-encoded chloroplast-targeted protein is hijacked by potyvirids as the scaffold protein to assemble a complex to facilitate viral movement across cells.Structure-guided design of VAR2CSA-based immunogens and a cocktail strategy for a placental malaria vaccineRui MaNichole D. SalinasSachy Orr-GonzalezBrandi RichardsonTarik OuahesHolly ToranoBethany J. JenkinsThayne H. DickeyJillian NealJunhui DuanRobert D. MorrisonApostolos G. GittisJustin Y. A. DoritchamouIrfan ZaidiLynn E. LambertPatrick E. DuffyNiraj H. Tolia10.1371/journal.ppat.10118792024-03-04T14:00:00Z2024-03-04T14:00:00Z<p>by Rui Ma, Nichole D. Salinas, Sachy Orr-Gonzalez, Brandi Richardson, Tarik Ouahes, Holly Torano, Bethany J. Jenkins, Thayne H. Dickey, Jillian Neal, Junhui Duan, Robert D. Morrison, Apostolos G. Gittis, Justin Y. A. Doritchamou, Irfan Zaidi, Lynn E. Lambert, Patrick E. Duffy, Niraj H. Tolia</p>
Placental accumulation of <i>Plasmodium falciparum</i> infected erythrocytes results in maternal anemia, low birth weight, and pregnancy loss. The parasite protein VAR2CSA facilitates the accumulation of infected erythrocytes in the placenta through interaction with the host receptor chondroitin sulfate A (CSA). Antibodies that prevent the VAR2CSA-CSA interaction correlate with protection from placental malaria, and VAR2CSA is a high-priority placental malaria vaccine antigen. Here, structure-guided design leveraging the full-length structures of VAR2CSA produced a stable immunogen that retains the critical conserved functional elements of VAR2CSA. The design expressed with a six-fold greater yield than the full-length protein and elicited antibodies that prevent adhesion of infected erythrocytes to CSA. The reduced size and adaptability of the designed immunogen enable efficient production of multiple variants of VAR2CSA for use in a cocktail vaccination strategy to increase the breadth of protection. These designs form strong foundations for the development of potent broadly protective placental malaria vaccines.<i>Candida albicans</i> translocation through the intestinal epithelial barrier is promoted by fungal zinc acquisition and limited by NFκB-mediated barrier protectionJakob L. SpragueTim B. SchilleStefanie AllertVerena TrümperAdrian LierPeter GroßmannEmily L. PriestAntzela TsavouGianni PanagiotouJulian R. NaglikDuncan WilsonSascha SchäubleLydia KasperBernhard Hube10.1371/journal.ppat.10120312024-03-01T14:00:00Z2024-03-01T14:00:00Z<p>by Jakob L. Sprague, Tim B. Schille, Stefanie Allert, Verena Trümper, Adrian Lier, Peter Großmann, Emily L. Priest, Antzela Tsavou, Gianni Panagiotou, Julian R. Naglik, Duncan Wilson, Sascha Schäuble, Lydia Kasper, Bernhard Hube</p>
The opportunistic fungal pathogen <i>Candida albicans</i> thrives on human mucosal surfaces as a harmless commensal, but frequently causes infections under certain predisposing conditions. Translocation across the intestinal barrier into the bloodstream by intestine-colonizing <i>C</i>. <i>albicans</i> cells serves as the main source of disseminated candidiasis. However, the host and microbial mechanisms behind this process remain unclear. In this study we identified fungal and host factors specifically involved in infection of intestinal epithelial cells (IECs) using dual-RNA sequencing. Our data suggest that host-cell damage mediated by the peptide toxin candidalysin-encoding gene <i>ECE1</i> facilitates fungal zinc acquisition. This in turn is crucial for the full virulence potential of <i>C</i>. <i>albicans</i> during infection. IECs in turn exhibit a filamentation- and damage-specific response to <i>C</i>. <i>albicans</i> infection, including NFκB, MAPK, and TNF signaling. NFκB activation by IECs limits candidalysin-mediated host-cell damage and mediates maintenance of the intestinal barrier and cell-cell junctions to further restrict fungal translocation. This is the first study to show that candidalysin-mediated damage is necessary for <i>C</i>. <i>albicans</i> nutrient acquisition during infection and to explain how IECs counteract damage and limit fungal translocation via NFκB-mediated maintenance of the intestinal barrier.The many faces of <i>Candida auris</i>: Phenotypic and strain variation in an emerging pathogenDarian J. SantanaGuolei ZhaoTeresa R. O’Meara10.1371/journal.ppat.10120112024-03-01T14:00:00Z2024-03-01T14:00:00Z<p>by Darian J. Santana, Guolei Zhao, Teresa R. O’Meara</p>
<i>Candida auris</i> is an emerging fungal pathogen with unusual evolutionary history—there are multiple distinct phylogeographic clades showing a near simultaneous transition from a currently unknown reservoir to nosocomial pathogen. Each of these clades has experienced different selective pressures over time, likely resulting in selection for genotypes with differential fitness or phenotypic consequences when introduced to new environments. We also observe diversification within clades, providing additional opportunities for phenotypic differences. These differences can have large impacts on pathogenic potential, drug resistance profile, evolutionary trajectory, and transmissibility. In recent years, there have been significant advances in our understanding of strain-specific behavior in other microbes, including bacterial and fungal pathogens, and we have an opportunity to take this strain variation into account when describing aspects of <i>C</i>. <i>auris</i> biology. Here, we critically review the literature to gain insight into differences at both the strain and clade levels in <i>C</i>. <i>auris</i>, focusing on phenotypes associated with clinical disease or transmission. Our goal is to integrate clinical and epidemiological perspectives with molecular perspectives in a way that would be valuable for both audiences. Identifying differences between strains and understanding which phenotypes are strain specific will be crucial for understanding this emerging pathogen, and an important caveat when describing the analysis of a singular isolate.Role of riboflavin deficiency in malaria pathophysiologyShweta SharmaArathy RamachandranAmit Sharma10.1371/journal.ppat.10119912024-03-01T14:00:00Z2024-03-01T14:00:00Z<p>by Shweta Sharma, Arathy Ramachandran, Amit Sharma</p>
The emergence of resistance against antimalarials and insecticides poses a significant threat to malaria elimination strategies. It is crucial to explore potential risk factors for malaria to identify new targets and alternative therapies. Malnutrition is a well-established risk factor for malaria. Deficiencies of micronutrients such as vitamin A, zinc, iron, folic acid, and phenotypic measures of malnutrition, such as stunting and wasting, have been studied extensively in the context of malaria. Vitamin B2, also known as riboflavin, is a micronutrient involved in maintaining cellular homeostasis. Riboflavin deficiency has been shown to have an inverse correlation with malarial parasitaemia. This article reviews the role of riboflavin in maintaining redox homeostasis and probes how riboflavin deficiency could alter malaria pathogenesis by disrupting the balance between oxidants and antioxidants. Though riboflavin analogues have been explored as antimalarials, new <i>in vivo</i> and patient-based research is required to target riboflavin-associated pathways for antimalarial therapy.The impact of HTLV-1 expression on the 3D structure and expression of host chromatinHiroko YaguchiAnat MelamedSaumya RamanayakeHelen KiikAviva WitkoverCharles R. M. Bangham10.1371/journal.ppat.10117162024-03-01T14:00:00Z2024-03-01T14:00:00Z<p>by Hiroko Yaguchi, Anat Melamed, Saumya Ramanayake, Helen Kiik, Aviva Witkover, Charles R. M. Bangham</p>
A typical HTLV-1-infected individual carries >10<sup>4</sup> different HTLV-1-infected T cell clones, each with a single-copy provirus integrated in a unique genomic site. We previously showed that the HTLV-1 provirus causes aberrant transcription in the flanking host genome and, by binding the chromatin architectural protein CTCF, forms abnormal chromatin loops with the host genome. However, it remained unknown whether these effects were exerted simply by the presence of the provirus or were induced by its transcription. To answer this question, we sorted HTLV-1-infected T-cell clones into cells positive or negative for proviral plus-strand expression, and then quantified host and provirus transcription using RNA-seq, and chromatin looping using quantitative chromosome conformation capture (q4C), in each cell population. We found that proviral plus-strand transcription induces aberrant transcription and splicing in the flanking genome but suppresses aberrant chromatin loop formation with the nearby host chromatin. Reducing provirus-induced host transcription with an inhibitor of transcriptional elongation allows recovery of chromatin loops in the plus-strand-expressing population. We conclude that aberrant host transcription induced by proviral expression causes temporary, reversible disruption of chromatin looping in the vicinity of the provirus.Ongoing evolution of the <i>Mycobacterium tuberculosis</i> lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressureSydney StanleyXin WangQingyun LiuYoung Yon KwonAbigail M. FreyNathan D. HicksAndrew J. VickersSheng HuiSarah M. Fortune10.1371/journal.ppat.10120502024-02-29T14:00:00Z2024-02-29T14:00:00Z<p>by Sydney Stanley, Xin Wang, Qingyun Liu, Young Yon Kwon, Abigail M. Frey, Nathan D. Hicks, Andrew J. Vickers, Sheng Hui, Sarah M. Fortune</p>
The bacterial determinants that facilitate <i>Mycobacterium tuberculosis</i> (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium <i>in vivo</i> by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is <i>lldD2</i>, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and <i>lldD2</i> is essential for Mtb growth in macrophages. We determined the extent of <i>lldD2</i> variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of <i>lldD2</i> evolution that occurs as a result of ongoing <i>lldD2</i> selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of <i>lldD2</i> additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved <i>lldD2</i> mutations functionally increase the quinone-dependent activity of LldD2. Using <sup>13</sup>C-lactate metabolic flux tracing, we find that <i>lldD2</i> is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of <i>lldD2</i>, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved <i>lldD2</i> variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to <i>lldD2</i> evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered <i>lldD2</i> activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of <i>lldD2</i> mutations in adapting to host stress.