Infected Host Cells Research Articles

Alterations of the gut microbiota in coronavirus disease 2019 and its therapeutic potential

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious threat to global health. SARS-CoV-2 infects host cells primarily by binding to angiotensin-converting enzyme 2, which is coexpressed in alveolar type 2 cells and gut epithelial cells. It is known that COVID-19 often presents with gastrointestinal symptoms and gut dysbiosis, mainly characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. In recent years, multiple studies have comprehensively explored gut microbiota alterations in COVID-19 and highlighted the clinical correlation between dysbiosis and COVID-19. SARS-CoV-2 causes gastrointestinal infections and dysbiosis mainly through fecal-oral transmission and the circulatory and immune pathways. Studies have shown that the gut microbiota and its metabolites can regulate the immune response and modulate antiviral effects. In addition, the gut microbiota is closely related to gastrointestinal symptoms, such as diarrhea, a common gastrointestinal symptom among COVID-19. Therefore, the contribution of the gut microbiota in COVID-19 should not be overlooked. Strategies targeting the gut microbiota via probiotics, prebiotics and fecal microbiota transplantation should be considered to treat this patient population in the future. However, the specific alterations and mechanisms as well as the contributions of gut microbiota in COVID-19 should be urgently further explored.

Biofilm Formation and its Association with Gram Negative Sepsis Pathogenicity

Background and objectives: Biofilm formation is an important virulence factor that protects an organism from antimicrobial agents as well as host immune effectors, thus allowing organisms to invade, survive, and cause persistent-reoccurring infection in host cells. The aim of this study was to investigate the ability of sepsis-causing gram-negative bacteria to form biofilms, evaluate the association between antibiotic resistance pattern and biofilm formation, determine the role and influence of biofilm formation on pathogenicity and clinical outcome of sepsis. Methods: A prospective study conducted from October 2020 to August 2021, non-replicated gram-negative bacteria isolates were recovered from blood samples of patients with suspected bacteremia, sepsis, and sepsis shock and identified using biochemical procedures. Antimicrobial susceptibility patterns of GNB isolates were determined using the Kirby-Bauer disc diffusion method and interpreted using CLSI guidelines. The ability of GNB isolates to form biofilm was assessed using Congo red agar and the tissue culture plate method. Results: Of the 160 Gram-negative bacteria tested, biofilm formation was seen in 73 (45.63%) isolates. Isolates are Klebsiella pneumoniae (39.73%), Acinetobacter spp. (34.25%), Escherichia coli (23.29%), Pseudomonas aeruginosa (1.37%), and other non-fermenters (1.37%). Isolates were highly resistant to cephalosporins, fluoroquinolones, and the penicillin group of antibiotics. No statistical relationship was found between resistance pattern, clinical outcome, and biofilm formation. Conclusion: In the current study, we found that 45.63% of gram-negative bacteria causing sepsis were biofilm producers. Klebsiella pneumonia isolates exhibited the highest levels of biofilm formation and antimicrobial resistance. Based on the strength of biofilm formation, most isolates were weak biofilm producers, and there was no statistical correlation between the formation of biofilms and antimicrobial resistance, indicating that the formation of biofilms was not a determining factor for resistance.

Characterization of SARS-CoV-2 Glycoprotein Using a Quantitative Cell-Cell Fusion System.

Coronaviruses (CoVs) infect host cells throughthe fusion of viral and cellular membrane and may also spread to the neighboring uninfected cells from infected cells through cell-cell fusion. The viral spike (S) glycoproteins play an essential role in mediating membrane fusion. Here, we present a luciferase-based quantitative assay to measurethe efficiency of cell-cell fusion mediated by theS protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This method applies to S proteins of theother coronaviruses and can be adapted to fusion proteins of other enveloped viruses.

Polystyrene microplastics significantly facilitate influenza A virus infection of host cells

Microplastics (MPs) are emerging pollutants which exist in various environments and pose a potential threat to human health. However, the effect of MP on respiratory pathogens-infected organisms is unknown. In order to explore the effect of MP on respiratory pathogen infection, we studied the effect of polystyrene microplastics (PS) on influenza A virus (IAV)-infected A549 cells. Western blot, qPCR, and viral plaque assay demonstrated that PS could promote IAV infection. Further study by bioluminescence imaging showed that a large number of IAV could be enriched on PS and entered cells through endocytosis. Meanwhile, the expression of IFITM3 in cells was significantly reduced. In addition, our results showed that PS down-regulated IRF3 and its active form P-IRF3 by down-regulating RIG-I and inhibiting TBK1 phosphorylation activation, which then significantly reduced IFN-β expression and affected the cellular innate antiviral immune system. Taken together, our results indicate the potential threat of MPs to respiratory diseases caused by IAV and provide new insights into human health protection.

COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants.

Antiviral defenses are one of the significant roles of RNA interference (RNAi) in plants. It has been reported that the host RNAi mechanism machinery can target viral RNAs for destruction because virus-derived small interfering RNAs (vsiRNAs) are found in infected host cells. Therefore, the recognition of plant vsiRNAs is the key to understanding the functional mechanisms of vsiRNAs and developing antiviral plants. In this work, we introduce a deep learning-based stacking ensemble approach, named computational prediction of plant exclusive virus-derived small interfering RNAs (COPPER), for plant vsiRNA prediction. COPPER used word2vec and fastText to generate sequence features and a hybrid deep learning framework, including a convolutional neural network, multiscale residual network and bidirectional long short-term memory network with a self-attention mechanism to enable precise predictions of plant vsiRNAs. Extensive benchmarking experiments with different sequence homology thresholds and ablation studies illustrated the comparative predictive performance of COPPER. In addition, the performance comparison with PVsiRNAPred conducted on an independent test dataset showed that COPPER significantly improved the predictive performance for plant vsiRNAs compared with other state-of-the-art methods. The datasets and source codes are publicly available at https://github.com/yuanyuanbu/COPPER.

C-Jun regulates flotillin 2 transcription to benefit viral accumulation in insect vectors

The c-Jun N-terminal kinase (JNK) signaling pathway plays a critical role in viral infection in host cells. In addition to triggering immune reactions against pathogens, the JNK signaling pathway has also been found to benefit viral infection. Our previous work showed that JNK activation facilitated rice stripe virus (RSV) accumulation in the insect vector small brown planthopper, but the underlying mechanisms remain elusive. Here, we revealed a link between JNK activation and the transcriptional upregulation of the plasma membrane protein flotillin 2, which mediates RSV cell entry. c-Jun, a downstream substrate of JNKs, was identified as a transcription factor that targets the promoter of flotillin 2 at three binding sites. Phosphorylated c-Jun, especially at the serine 63 site, promoted the transcriptional activity of c-Jun on flotillin 2. JNK activation or inhibition affected c-Jun phosphorylation status and flotillin 2 expression. In the midguts of planthoppers, RSV infection significantly increased flotillin 2 expression and the phosphorylation level of JNKs and c-Jun. Manipulation of JNK status impacted viral acquisition in midgut cells. These findings reveal a new regulatory mechanism of the JNK signaling pathway and shed light on the virus-supportive effect of this pathway.

Identification of the Intrinsic Motions and Related Key Residues Responsible for the Twofold Channel Opening of Poliovirus Capsid by Using an Elastic Network Model Combined with an Internal Coordinate.

Poliovirus (PV) is an infectious virus that causes poliomyelitis, which seriously threatens the health of children. The release of viral RNA is a key step of PV in host cell infection, and multiple lines of evidence have demonstrated that RNA release is initiated by the opening of the twofold channels of the PV capsid. However, the mechanism that controls the twofold channel opening is still not well understood. In addition, the channel opening motion of the recombinant PV capsid leads to the destruction of predominant neutralizing epitopes and thus hinders the capsid as a vaccine immunogen. Therefore, it is important to identify the intrinsic motions and the related key residues controlling the twofold channel opening for understanding the virus infection mechanism and developing capsid-based vaccines. In the present work, the width of the channel was selected as an internal coordinate directly related to the channel opening, and then the elastic network model (ENM) combined with the group theory were employed to extract the intrinsic motion modes that mostly contribute to the opening of the twofold channels. Our results show that the channel opening predominately induced by the breathing motion and the overall rotation of each protomer in the capsid. Then, an internal coordinate-based perturbation method was used to identify the key residues regulating the twofold channel opening of PV. The calculation results showed that the predicted key residues are mainly located at the twofold axes, the bottom of the canyons and the quasi threefold axes. Our study is helpful for better understanding the twofold channel opening mechanism and provides a potential target for preventing the opening of the channels, which is of great significance for PV vaccine design. The source code of this study is available at https://github.com/SJGLAB/CapsidKeyRes.git.

2073. Persistent HIV-1 Viremia Despite Intensive Antiviral Therapy Due to Non-responsive Clonal Viral Lineages

Abstract Background After initiation of antiviral therapy (ART), plasma HIV-1 RNA is usually undetectable after one month. In rare cases, viral suppression may not be achieved despite good adherence and with virus susceptible to ART. We used ultra-deep Primer ID next gen sequencing (NGS) to study the viral population and evolution of HIV-1 in two patients with persistent viremia on intensive ART. Methods We extracted viral RNA from plasma samples collected at multiple timepoints over the duration of the treatment from two patients (VEX1 and VEX2). We constructed Primer ID NGS libraries covering part of the pol gene and the env V1/V3 region and sequenced them on the Illumina MiSeq platform. We used the ‘tcs’ pipeline to construct template consensus sequences (TCS) for each region, and searched for drug resistance mutations (DRMs). The Geno2pheno pipeline was used to predict co-receptor tropisms. Results Patient VEX1 was followed for two years on ART. VEX2 restarted ART in the hospital and received directly observed therapy for nearly 6 months. Both had over 1 million viral copies/mL at the initiation of ART, and the CD4 cell counts were extremely low. Their viral loads slowly declined to approx. 10,000 copies/mL at the end of follow-up but complete viral suppression was not achieved for either patient despite appropriate ART. DRMs were not detected in either patient throughout the treatment with detection sensitivity as low as 0.1%. The sequencing results for VEX1 showed that there were both X4- and R5-tropic viruses at all timepoints and R5 viruses decayed much more slowly than X4 viruses, up to 35-fold more slowly in the initial 3 months of ART. Phylogenetic analysis revealed that the persistent R5 viruses were largely clonal while little clonality was found in the persistent X4 virus. In VEX2, all viruses were R5-tropic. There were three major distinct lineages in the viral population, and two of them completely disappeared after the initiation of ART while the other lineage persisted throughout therapy (Fig 1). The persistent lineage in VEX2 was highly clonal. Pooled maximum likelihood tree at env V1V3 region of 3 time points from patient VEX2. Sequences in red were from 2018 when we obtained the initial specimen from the patient. Sequences in blue were from Sept 2021 when the patient restarted ART. Sequences in green were from Oct 2021 when the patient were on ART for 3 weeks. The patient had 3 major viral lineages, L1, L2, and L3. From 2018 to Sept 2021, we could see the viral evolution of the three lineages (blue arrows). After 3 weeks of ART, L1 and L2 disappeared, while the L3 persisted. We could also see that L3 had several clonal populations which did not respond to ART nor evolve from 2018 to 2021. The additional sequences from Nov 2021 to Feb 2022 were identical to the sequences obtained on Oct 2021 (not shown on this figure). Conclusion Our study shows that persistent viremia on ART can come from clonal viral lineages that carry no DRMs. Clonally expanded and infected host cells might contribute to the phenomenon. Further study is needed to explore the origin of these clonal viral genomes. Disclosures Jonathan Parr, MD, Abbott Laboratories: Donation of laboratory testing and reagents|Gilead Sciences: Grant/Research Support|Virology Education: Honoraria|World Health Organization: Advisor/Consultant|World Health Organization: Grant/Research Support David A. Wohl, M.D., Gilead: Advisor/Consultant|Gilead: Grant/Research Support|Janssen: Advisor/Consultant|Lilly: Grant/Research Support|Merck: Grant/Research Support|ViiV: Advisor/Consultant|ViiV: Grant/Research Support Joseph J. Eron, MD, Adagio Therapeutics: data safety monitoring committee|Gilead Sciences: Advisor/Consultant|Gilead Sciences: Grant/Research Support|Glaxo Smith Kline: Advisor/Consultant|Merck: Advisor/Consultant|ViiV Healthcare: Advisor/Consultant|ViiV Healthcare: Grant/Research Support.

504. Latent HHV7 Infection Attenuates Beneficial Host-Microbe Interactions in the Human Gut

Abstract Background Human Herpes Virus 7 (HHV7) infection results in a lifelong latent infection with over 95% of adults seropositive for HHV7. Lymphocytes are the best understood host cell type for latent HHV7, with the gastric mucosa another site of latent infection. Herpesviridae latency affects host processes like interferon signaling, antigen presentation, and proliferation—the same host pathways are implicated in the beneficial responses to commensal microbes. Methods Adult human colonic organoids with or without latent HHV7 infection were co-cultured with B. longum in asymmetric oxygen conditions that allow for live interaction (F1). The transcriptional state after 24h of interactions was determined with RNA-sequencing. The transcriptional state was compared between axenic (no microbes) or after co-culture and with or without latent HHV7. F1: Establishing oxygen gradients across epithelial monolayers (A) Schematic of oxygen gradient apparatus (B) Closeup view of individual well (C) Growth of the anaerobe B. longum was identical in the apparatus with hypoxic epithelial compared to full anaerobic growth (D) Butyrate administration protects the epithelium from inflammatory effects of deoxycholate. Results Screening human intestinal organoids (that lack lymphocytes and are strictly of the endodermal lineage) we have generated evidence that intestinal stem cells (ISC) and IEC can be a host cell for latent HHV7 infection in some but not all people (T1). RNA-sequencing reveals that this is true latency, with ISC and IEC containing HHV7 without transcripts from any of the protein-coding genes in the HHV7 genome. Further we have observed that latent HHV7 is mosaic in the gut, not affecting all of the ISC in an individual (T1). In organoid-derived human IEC we have noted co-culture with the commensal bacteria B. longum suppresses key executors of apoptosis and pyroptosis (F2). These same effects are no longer observed with the B. longum is interacting with IEC latently infected with HHV7. A similar pattern was observed with NFkB regulators (F3). T1: Latent HHV7 is found in some intestinal organoids derived from healthy adults From the University of Michigan Translational Tissue Modeling Laboratory (TTML) organoid registry. Each donor is assigned a unique numerical ID. Viral panel is from a commercial multiplex PCR screen. Notably, donor 87 has colonic organoids with and without latent HHV7. F2: Co-culture with the commensal microbe B. longum suppresses most apoptosis and pyroptosis executors only in an organoid without latent HHV7 infection. Fragments per kilobase per millions of reads (FPKM) from RNA-sequencing of fully-differentiated organoid-derived human intestinal epithelium after 24 hours of co-culture with B.longum (Orange) or remaining axenic (without microbes; Blue). Results from cell without (left) or with (right) latent HHV7. F3: Stimulation of the NFkB inhibitor NFKBIA by co-culture with the commensal microbe B. longum is absent in organoids with latent HHV7 infection. Fragments per kilobase per millions of reads (FPKM) from RNA-sequencing of fully-differentiated organoid-derived human intestinal epithelium after 24 hours of co-culture with B.longum (Orange) or remaining axenic (without microbes; Blue). Results from cell without (left) or with (right) latent HHV7. Conclusion Latent HHV7 in the human gut epithelium may attenuate the effect of beneficial microbes like B. longum (F4). The evidence for mosaicism of latent HHV7 in the human gut adds a spatial aspect to these attenuating effects that could be relevant for specific disease processes (e.g. skip lesions in Crohn’s disease). Confirmation of these findings, estimating the true prevalence of latent HHV7 in the gut, and identification of the HHV7 latency mechanism will be required to understand the full implications of these findings. F4: A Model of Latent HHV7 Infection Attenuating Responses to Commensal Microbes. Based on our findings, latent HHV7 infection in the intestinal epithelium may leave the gut mucosa at increased risk for injury by impairing the beneficial response to commensal microbes in a spatially complex manner due to the apparent mosaic nature of latent HHV7 infection in the gut. Disclosures Jonathan L. Golob, MD/PhD, Loxo Oncology: Employment of Spouse.

Therapeutic Applications for Oncolytic Self-Replicating RNA Viruses.

Self-replicating RNA viruses have become attractive delivery vehicles for therapeutic applications. They are easy to handle, can be rapidly produced in large quantities, and can be delivered as recombinant viral particles, naked or nanoparticle-encapsulated RNA, or plasmid DNA-based vectors. The self-replication of RNA in infected host cells provides the means for generating much higher transgene expression levels and the possibility to apply substantially reduced amounts of RNA to achieve similar expression levels or immune responses compared to conventional synthetic mRNA. Alphaviruses and flaviviruses, possessing a single-stranded RNA genome of positive polarity, as well as measles viruses and rhabdoviruses with a negative-stranded RNA genome, have frequently been utilized for therapeutic applications. Both naturally and engineered oncolytic self-replicating RNA viruses providing specific replication in tumor cells have been evaluated for cancer therapy. Therapeutic efficacy has been demonstrated in animal models. Furthermore, the safe application of oncolytic viruses has been confirmed in clinical trials. Multiple myeloma patients treated with an oncolytic measles virus (MV-NIS) resulted in increased T-cell responses against the measles virus and several tumor-associated antigen responses and complete remission in one patient. Furthermore, MV-CEA administration to patients with ovarian cancer resulted in a stable disease and more than doubled the median overall survival.

Host autophagy limits Toxoplasma gondii proliferation in the absence of IFN-γ by affecting the hijack of Rab11A-positive vesicles.

Autophagy has been recognized as a bona fide immunological process. Evidence has shown that this process in IFN-γ stimulated cells controls Toxoplasma gondii proliferation or eliminates its infection. However, little is known about the effect of T. gondii infection on the host cell autophagy in the absence of IFN-γ. Multiple autophagy detection methods and CRISPR/CAS9 technology were used to study T. gondii-induced autophagy in HeLa and several other mammalian cell lines. Here, we report increased LC3 II, autophagosome-like membrane structures, enhanced autophagic flux, and decreased lysosomes in a range of mammalian cell lines without IFN-γ treatment after T. gondii infection. Specifically, disruption of host atg5 (a necessary gene for autophagy) in HeLa cells promoted the intracellular replication of T. gondii, with the transcript level of rab11a increased, compared with that in wild-type cells. Further, after T. gondii infection, the abundance of Rab11A remained stable in wild-type HeLa cells but decreased in atg5 -/- mutant. Disruption of rab11a in the HeLa cells compromised the proliferation of T. gondii, and increased the transcription of gra2 in the parasite. Compared to the T. gondii wild-type RH∆ku80 strain, the ∆gra2 mutant induces enhanced host autophagy in HeLa cells, and results in slower replication of the parasite. Collectively, these results indicate that host cell autophagy can limit T. gondii proliferation in an IFN-γ independent manner, possibly by affecting the hijack of host Rab11A-positive vesicles by the parasite which involved TgGRA2. The findings provide novel insights into T. gondii infection in host cells and toxoplasmosis research.

A genetically engineered, stem-cell-derived cellular vaccine

Despite rapid clinical translation of COVID-19 vaccines in response to the global pandemic, an opportunity remains for vaccine technology innovation to address current limitations and meet challenges of inevitable future pandemics. We describe a universal vaccine cell (UVC) genetically engineered to mimic natural physiological immunity induced upon viral infection of host cells. Cells engineered to express the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike as a representative viral antigen induce robust neutralizing antibodies in immunized non-human primates. Similar titers generated in this established non-human primate (NHP) model have translated into protective human neutralizing antibody levels in SARS-CoV-2-vaccinated individuals. Animals vaccinated with ancestral spike antigens and subsequently challenged with SARS-CoV-2 Delta variant in a heterologous challenge have an approximately 3 log decrease in viral subgenomic RNA in the lungs. This cellular vaccine is designed as a scalable cell line with a modular poly-antigenic payload, allowing for rapid, large-scale clinical manufacturing and use in an evolving viral variant environment.

The coordination of anti-phage immunity mechanisms in bacterial cells

Bacterial cells are equipped with a variety of immune strategies to fight bacteriophage infections. Such strategies include unspecific mechanisms directed against any phage infecting the cell, ranging from the identification and cleavage of the viral DNA by restriction nucleases (restriction-modification systems) to the suicidal death of infected host cells (abortive infection, Abi). In addition, CRISPR-Cas systems generate an immune memory that targets specific phages in case of reinfection. However, the timing and coordination of different antiviral systems in bacterial cells are poorly understood. Here, we use simple mathematical models of immune responses in individual bacterial cells to propose that the intracellular dynamics of phage infections are key to addressing these questions. Our models suggest that the rates of viral DNA replication and cleavage inside host cells define functional categories of phages that differ in their susceptibility to bacterial anti-phage mechanisms, which could give raise to alternative phage strategies to escape bacterial immunity. From this viewpoint, the combined action of diverse bacterial defenses would be necessary to reduce the chances of phage immune evasion. The decision of individual infected cells to undergo suicidal cell death or to incorporate new phage sequences into their immune memory would be determined by dynamic interactions between the host’s immune mechanisms and the phage DNA. Our work highlights the importance of within-cell dynamics to understand bacterial immunity, and formulates hypotheses that may inspire future research in this area.

Duck TRIM35 Promotes Tembusu Virus Replication by Interfering with RIG-I-Mediated Antiviral Signaling in Duck Embryo Fibroblasts.

In China, the duck industry has been severely impacted by the newly emerging duck Tembusu virus (DTMUV). For DTMUV to successfully infect host cells, it employs several strategies that subvert the host's innate immune response. It has been found that several viral proteins encoded by DTMUV have strategically targeted the crucial molecules of the RIG-I-like Receptor (RLR) signaling pathway to antagonize host antiviral responses. However, it is not well known how the host proteins manipulated by DTMUV contribute to innate immune evasion. The present study reports that duck TRIM35 (duTRIM35) antagonizes DTMUV-induced innate immune responses by targeting duck RIG-I (duRIG-I) in duck embryo fibroblasts. A significant increase in duTRIM35 expression occurred during DTMUV infection. DuTRIM35 overexpression suppressed DTMUV-triggered expression of interferon beta (IFN-β) and interferon-stimulated genes (ISGs), promoting viral replication, whereas knockdown of duTRIM35 augments the innate immune response, reducing viral replication. Furthermore, duTRIM35 significantly impaired the IFN-β expression mediated by duRIG-I but not by other RLR signaling molecules. Mechanistically, duTRIM35 interfered with duRIG-I-duTRIM25 interaction and impeded duTRIM25-mediated duRIG-I ubiquitination by interacting with both duRIG-I and duTRIM25. Our findings indicate that duTRIM35 expression induced by DTMUV infection interfered with the duRIG-I-mediated antiviral response, illustrating a novel strategy in which DTMUV can evade the host's innate immunity. IMPORTANCE Duck Tembusu virus (DTMUV), an emerging flavivirus pathogen causing a substantial drop in egg production and severe neurological disorders in duck populations, has led to massive economic losses in the global duck industry. DTMUV has employed various strategies to subvert the host's innate immune response to establish a productive infection in host cells. In this study, we report that duck TRIM35 (duTRIM35) expression was upregulated upon DTMUV infection in vitro and in vivo, and its expression antagonized DTMUV-induced innate immune responses by targeting duck RIG-I (duRIG-I) in duck embryo fibroblasts. Further studies suggest that duTRIM35 interfered with duRIG-I-duTRIM25 interaction and impeded duTRIM25-mediated duRIG-I ubiquitination by interacting with both duRIG-I and duTRIM25. Together, these results revealed that duTRIM35 expression induced by DTMUV infection downregulated duRIG-I-mediated host antiviral response, which elucidated a novel strategy of DTMUV for innate immune evasion.

SARS-CoV-2 Antibody Effectiveness Is Influenced by Non-Epitope Mutation/Binding-Induced Denaturation of the Epitope 3D Architecture.

The public health threat from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to intensify with emerging variants of concern (VOC) aiming to render COVID-19 vaccines/infection-induced antibodies redundant. The SARS-CoV-2 spike protein is responsible for receptor binding and infection of host cells making it a legitimate antibody target. Antibodies mostly target epitopes in the receptor binding domain (RBD). Mutations occurring within epitopes influence antibody specificity and function by altering their 3D architecture. However, the mechanisms by which non-epitope mutations in the RBD influence antibody specificity and function remain a mystery. We used Protein Data Bank (PDB) deposited 3D structures for the original, Beta, Delta, BA.1, and BA.2 RBD proteins in complex with either neutralizing antibodies or Angiotensin-Converting Enzyme 2 (ACE2) to elucidate the structural and mechanistic basis for neutralizing antibody evasion driven by non-epitope amino acid substitutions in the RBD. Since the mechanism behind the extensively reported functional discrepancies between the same antibody when used individually and when used in an antibody cocktail is lacking, we explored the structural basis for this inconsistency. Finally, since SARS-CoV-2 antibodies are viral mutagens, we deciphered determinants for antibody-pressured amino acid substitutions. On the one hand, we show that non-epitope mutations in the RBD domain of SARS-CoV-2 VOC influence the formation of hydrogen bonds in the paratope-epitope interface by repositioning RBD amino-acid sidechains (AASCs). This increases the distance between complementary donor/acceptor atoms on paratope and epitope AASCs leading to weaker or the complete prevention of the formation of hydrogen bonds in the paratope-epitope interface. On the other hand, we show that SARS-CoV-2 VOC employ the same strategy to simultaneously search for complementary donor/acceptor atoms on ACE2 AASCs to form new interactions, potentially favoring increased viral transmission. Additionally, we illustrate that converting the spike protein to an RBD, a deletion mutation, also repositions epitope AASCs and that AASC interactions in the paratope-epitope interface vary when an antibody is used individually versus when utilized as a cocktail with other antibodies. Finally, we show that the process of substituting immunogenic RBD amino acids begins with the repositioning of their AASCs induced by immune/antibody pressure. We show that donor/acceptor atoms from any amino acid can determine cross-reactivity instead, provided they possess and present spatially pairing donor/acceptor atoms. By studying structural alignments for PDB deposited antibody-RBD 3D structures and relating them to published binding and neutralization profiles of the same antibodies, we demonstrate that minor structural alterations such as epitope AASC repositioning have a major impact on antibody effectiveness and, hence, should receive adequate attention given that protein structure dictates protein function.

Host Cell Oxidative Stress Promotes Intracellular Fluoroquinolone Persisters of Streptococcus pneumoniae.

Bacterial persisters represent a small subpopulation that tolerates high antibiotic concentrations without acquiring heritable resistance, and it may be generated by environmental factors. Here, we report the first antibiotic persistence mechanism in Streptococcus pneumoniae, which is induced by oxidative stress conditions and allows the pneumococcus to survive in the presence of fluoroquinolones. We demonstrated that fluoroquinolone persistence is prompted by both the impact of growth arrest and the oxidative stress response induced by H2O2 in bacterial cells. This process protected pneumococci against the deleterious effects of high ROS levels induced by fluoroquinolones. Importantly, S. pneumoniae develops persistence during infection, and is dependent on the oxidative stress status of the host cells, indicating that its transient intracellular life contributes to this mechanism. Furthermore, our findings suggest persistence may influence the outcome of antibiotic therapy and be part of a multistep mechanism in the evolution of fluoroquinolone resistance. IMPORTANCE In S. pneumoniae, different mechanisms that counteract antibiotic effects have been described, such as vancomycin tolerance, heteroresistance to penicillin and fluoroquinolone resistance, which critically affect the therapeutic efficacy. Antibiotic persistence is a type of antibiotic tolerance that allows a bacterial subpopulation to survive lethal antimicrobial concentrations. In this work, we used a host-cell infection model to reveal fluoroquinolone persistence in S. pneumoniae. This mechanism is induced by oxidative stress that the pneumococcus must overcome to survive in host cells. Many fluoroquinolones, such as levofloxacin and moxifloxacin, have a broad spectrum of activity against bacterial pathogens of community-acquired pneumonia, and they are used to treat pneumococcal diseases. However, the emergence of fluoroquinolone-resistant strains complicates antibiotic treatment of invasive infections. Consequently, antibiotic persistence in S. pneumoniae is clinically relevant due to prolonged exposure to fluoroquinolones likely favors the acquisition of mutations that generate antibiotic resistance in persisters. In addition, this work contributes to the knowledge of antibiotic persistence mechanisms in bacteria.

Extracellular vesicles of Candida albicans regulate its own growth through the L-arginine/nitric oxide pathway.

Candida albicans is the main conditional pathogenic fungus among the human microbiome. Extracellular vesicles (EVs) secreted by C. albicans are important for its pathogenesis. However, the effects and mechanisms of EVs on C. albicans own growth are not clear. Here, we isolated EVs from C. albicans cells grown in four culture media, including RPMI 1640, DMEM, YPD, and YNB, and measured their effects on the own growth of C. albicans in these media. All the C. albicans EVs from the four media could promote the growth of C. albicans in RPMI 1640 and DMEM media, but had no effects in YPD and YNB media, indicating that the effects of EVs on C. albicans growth were dependent on some media contents. By comparing the media contents and transcriptome analysis, arginine was identified as the key factor for the growth promotion of C. albicans EVs. EVs activated the L-arginine/nitric oxide pathway to promote the growth of C. albicans through that EVs increased the NO levels and upregulated the expression of NO dioxygenase gene YHB1 to reduce the intracellular reactive oxygen species (ROS) and cell apoptosis. During the host cell infections, C. albicans EVs synergistically enhanced the destructive effects of C. albicans to host cells, including RAW264.7, HOK, TR146, and HGEC, suggesting that the growth promotion by EVs enhanced the pathogenesis of C. albicans. Our results demonstrated the important roles of EVs on C. albicans own growth for the first time and highlight its synergism with C. albicans to increase the pathogenesis. KEY POINTS: • C. albicans extracellular vesicles (EVs) promoted its own growth. • EVs activated the l-arginine/NO pathway to reduce ROS and apoptosis of C. albicans. • EVs enhanced the damage to the host cell caused by C. albicans.

Host Cell Amplification of Nutritional Stress Contributes To Persistence in Chlamydia trachomatis.

Persistence, a viable but non-replicating growth state, has been implicated in diseases caused by Chlamydia trachomatis. Starvation of distinct nutrients produces a superficially similar persistent state, implying convergence on a common intracellular environment. We employed host-pathogen dual RNA-sequencing under both iron- and tryptophan-starved conditions to systematically characterize the persistent chlamydial transcriptome and to define common contributions of the host cell transcriptional stress response in shaping the intracellular environment. The transcriptome of the infected host cells was highly specific to each nutritional stress, despite comparable effects on chlamydial growth and development in each condition. In contrast, the chlamydial transcriptomes between nutritional conditions were highly similar, suggesting some overlap in host cell responses to iron limitation and tryptophan starvation that contribute to a common persistent phenotype. We demonstrate that a commonality in the host cell responses is the suppression of GTP biosynthesis, a nucleotide for which Chlamydia are auxotrophic. Pharmacological inhibition of host IMP dehydrogenase (IMPDH1), which catalyzes the rate-limiting step in de novo guanine nucleotide synthesis, resulted in comparable GTP depletion to both iron and tryptophan starvation and induced chlamydial persistence. Moreover, IMPDH1 inhibition and iron starvation acted synergistically to control chlamydial growth. Thus, host cell reduction in GTP levels amplifies the nutritional stress to intracellular chlamydiae in infection-relevant models of persistence, illustrating the determinative role the infected host cell plays in bacterial stress responses. IMPORTANCE Bacteria respond to nutritional stress through universal and unique mechanisms. Genome reduction in the Chlamydiaceae, a consequence of coevolution with their obligate eukaryotic hosts, has reduced their repertoire of stress response mechanisms. Here, we demonstrate that the infected host cell may provide the context within which universal stress responses emerge for Chlamydia trachomatis. We report that during starvation of the essential nutrients iron or tryptophan, a common response of the infected epithelial cell is the suppression of GTP biosynthesis, which induces a persistent developmental state in the pathogen. Thus, chlamydial persistence results from the combined effects of primary stresses on the pathogen and the host, with the latter eliciting a secondary host cell response that intensifies the inhospitable intracellular environment.

Exposure to stressors and antimicrobials induces cell-autonomous ultrastructural heterogeneity of an intracellular bacterial pathogen.

Despite their clonality, intracellular bacterial pathogens commonly show remarkable physiological heterogeneity during infection of host cells. Physiological heterogeneity results in distinct ultrastructural morphotypes, but the correlation between bacterial physiological state and ultrastructural appearance remains to be established. In this study, we showed that individual cells of Salmonella enterica serovar Typhimurium are heterogeneous in their ultrastructure. Two morphotypes based on the criterion of cytoplasmic density were discriminated after growth under standard culture conditions, as well as during intracellular lifestyle in mammalian host cells. We identified environmental conditions which affect cytoplasmic densities. Using compounds generating oxygen radicals and defined mutant strains, we were able to link the occurrence of an electron-dense ultrastructural morphotype to exposure to oxidative stress and other stressors. Furthermore, by combining ultrastructural analyses of Salmonella during infection and fluorescence reporter analyses for cell viability, we provided evidence that two characterized ultrastructural morphotypes with electron-lucent or electron-dense cytoplasm represent viable cells. Moreover, the presence of electron-dense types is stress related and can be experimentally induced only when amino acids are available in the medium. Our study proposes ultrastructural morphotypes as marker for physiological states of individual intracellular pathogens providing a new marker for single cell analyses.

Aptamer-Mediated Antiviral Approaches for SARS-CoV-2.

2020 and 2021 were disastrous years across the world, with the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) virus as a pandemic, which continues to be a top global health issue. There are still many countries and regions struggling to fight coronavirus disease 2019 (COVID-19), and, with the emergence of the various variants of the virus, we are still far from considering this global pandemic over. In addition to having good diagnostic tools and a variety of vaccines with high efficacy, it is of utmost importance to develop effective antiviral drugs or therapies to battle COVID-19. Aptamers known as the next-generation targeting elements can offer promising opportunities in developing antiviral drugs against SARS-CoV-2. This is owing to their high specificity and affinity, making them ideal for targeting ligands and neutralizers to impede both, viral entry and replication or even further enhance the anti-infection effects in the infected host cells. Also, aptamers are extremely attractive as they can be rapidly synthesized and scalable with a lower production cost. This work provides in-depth discussions on the potential of aptamers in therapeutic applications, their mode of action, and current progress on the use of aptamer-based therapies against SARS-CoV-2 and other viruses. The article also discusses the limitations associated with aptamer-based SARS-CoV-2-antiviral therapy with several proposed ideas to resolve them. Lastly, theranostic applications of aptamer nanoformulated dendrimers against viral infections are discussed.