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Annual Review of Microbiology Sep 2022Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacteria that consist of a growth-inhibiting toxin and its cognate antitoxin. These systems are prevalent... (Review)
Review
Toxin-antitoxin (TA) systems are ubiquitous genetic elements in bacteria that consist of a growth-inhibiting toxin and its cognate antitoxin. These systems are prevalent in bacterial chromosomes, plasmids, and phage genomes, but individual systems are not highly conserved, even among closely related strains. The biological functions of TA systems have been controversial and enigmatic, although a handful of these systems have been shown to defend bacteria against their viral predators, bacteriophages. Additionally, their patterns of conservation-ubiquitous, but rapidly acquired and lost from genomes-as well as the co-occurrence of some TA systems with known phage defense elements are suggestive of a broader role in mediating phage defense. Here, we review the existing evidence for phage defense mediated by TA systems, highlighting how toxins are activated by phage infection and how toxins disrupt phage replication. We also discuss phage-encoded systems that counteract TA systems, underscoring the ongoing coevolutionary battle between bacteria and phage. We anticipate that TA systems will continue to emerge as central players in the innate immunity of bacteria against phage.
Topics: Antitoxins; Bacteria; Bacterial Proteins; Bacterial Toxins; Bacteriophages; Plasmids; Toxin-Antitoxin Systems
PubMed: 35395167
DOI: 10.1146/annurev-micro-020722-013730 -
Nature Feb 2022The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires...
The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A-F)-a grouping that is highly concordant with knowledge-based structural classifications. Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A-D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309) and group F (for example, CR3022), which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.
Topics: Angiotensin-Converting Enzyme 2; Antibodies, Monoclonal; Antibodies, Neutralizing; Antibodies, Viral; COVID-19; COVID-19 Vaccines; Cells, Cultured; Convalescence; Epitopes, B-Lymphocyte; Humans; Immune Evasion; Immune Sera; Models, Molecular; Mutation; Neutralization Tests; SARS-CoV-2; Spike Glycoprotein, Coronavirus
PubMed: 35016194
DOI: 10.1038/s41586-021-04385-3 -
Nature Dec 2023A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant, BA.2.86, has emerged and spread to numerous countries worldwide, raising alarm...
A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant, BA.2.86, has emerged and spread to numerous countries worldwide, raising alarm because its spike protein contains 34 additional mutations compared with its BA.2 predecessor. We examined its antigenicity using human sera and monoclonal antibodies (mAbs). Reassuringly, BA.2.86 was no more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, indicating that the new subvariant would not have a growth advantage in this regard. Importantly, sera from people who had XBB breakthrough infection exhibited robust neutralizing activity against all viruses tested, suggesting that upcoming XBB.1.5 monovalent vaccines could confer added protection. Although BA.2.86 showed greater resistance to mAbs to subdomain 1 (SD1) and receptor-binding domain (RBD) class 2 and 3 epitopes, it was more sensitive to mAbs to class 1 and 4/1 epitopes in the 'inner face' of the RBD that is exposed only when this domain is in the 'up' position. We also identified six new spike mutations that mediate antibody resistance, including E554K that threatens SD1 mAbs in clinical development. The BA.2.86 spike also had a remarkably high receptor affinity. The ultimate trajectory of this new SARS-CoV-2 variant will soon be revealed by continuing surveillance, but its worldwide spread is worrisome.
Topics: Humans; Antibodies, Monoclonal; Antibodies, Neutralizing; Antibodies, Viral; COVID-19; COVID-19 Vaccines; Epitopes, B-Lymphocyte; Immunogenicity, Vaccine; Mutation; Receptors, Virus; SARS-CoV-2; Spike Glycoprotein, Coronavirus; Immune Sera
PubMed: 37871613
DOI: 10.1038/s41586-023-06750-w -
Emerging Microbes & Infections Dec 2020Pseudoviruses are useful virological tools because of their safety and versatility, especially for emerging and re-emerging viruses. Due to its high pathogenicity and...
Pseudoviruses are useful virological tools because of their safety and versatility, especially for emerging and re-emerging viruses. Due to its high pathogenicity and infectivity and the lack of effective vaccines and therapeutics, live SARS-CoV-2 has to be handled under biosafety level 3 conditions, which has hindered the development of vaccines and therapeutics. Based on a VSV pseudovirus production system, a pseudovirus-based neutralization assay has been developed for evaluating neutralizing antibodies against SARS-CoV-2 in biosafety level 2 facilities. The key parameters for this assay were optimized, including cell types, cell numbers, virus inoculum. When tested against the SARS-CoV-2 pseudovirus, SARS-CoV-2 convalescent patient sera showed high neutralizing potency, which underscore its potential as therapeutics. The limit of detection for this assay was determined as 22.1 and 43.2 for human and mouse serum samples respectively using a panel of 120 negative samples. The cutoff values were set as 30 and 50 for human and mouse serum samples, respectively. This assay showed relatively low coefficient of variations with 15.9% and 16.2% for the intra- and inter-assay analyses respectively. Taken together, we established a robust pseudovirus-based neutralization assay for SARS-CoV-2 and are glad to share pseudoviruses and related protocols with the developers of vaccines or therapeutics to fight against this lethal virus.
Topics: Animals; Antibodies, Neutralizing; Antibodies, Viral; Betacoronavirus; COVID-19; Cell Line; Coronavirus Infections; Humans; Immune Sera; Immunization, Passive; Limit of Detection; Membrane Glycoproteins; Mice; Neutralization Tests; Plasmids; Pneumonia, Viral; Reproducibility of Results; SARS-CoV-2; Sensitivity and Specificity; Spike Glycoprotein, Coronavirus; Vesicular stomatitis Indiana virus; Viral Envelope Proteins; Virus Internalization; COVID-19 Serotherapy
PubMed: 32207377
DOI: 10.1080/22221751.2020.1743767 -
Journal of Virology Jan 2022A comprehensive analysis and characterization of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection model that mimics non-severe and severe...
A comprehensive analysis and characterization of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection model that mimics non-severe and severe coronavirus disease 2019 (COVID-19) in humans is warranted for understating the virus and developing preventive and therapeutic agents. Here, we characterized the K18-hACE2 mouse model expressing human (h)ACE2 in mice, controlled by the human keratin 18 (K18) promoter, in the epithelia, including airway epithelial cells where SARS-CoV-2 infections typically start. We found that intranasal inoculation with higher viral doses (2 × 10 and 2 × 10 PFU) of SARS-CoV-2 caused lethality of all mice and severe damage of various organs, including lung, liver, and kidney, while lower doses (2 × 10 and 2 × 10 PFU) led to less severe tissue damage and some mice recovered from the infection. In this hACE2 mouse model, SARS-CoV-2 infection damaged multiple tissues, with a dose-dependent effect in most tissues. Similar damage was observed in postmortem samples from COVID-19 patients. Finally, the mice that recovered from infection with a low dose of virus survived rechallenge with a high dose of virus. Compared to other existing models, the K18-hACE2 model seems to be the most sensitive COVID-19 model reported to date. Our work expands the information available about this model to include analysis of multiple infectious doses and various tissues with comparison to human postmortem samples from COVID-19 patients. In conclusion, the K18-hACE2 mouse model recapitulates both severe and non-severe COVID-19 in humans being dose-dependent and can provide insight into disease progression and the efficacy of therapeutics for preventing or treating COVID-19. The pandemic of coronavirus disease 2019 (COVID-19) has reached nearly 240 million cases, caused nearly 5 million deaths worldwide as of October 2021, and has raised an urgent need for the development of novel drugs and therapeutics to prevent the spread and pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To achieve this goal, an animal model that recapitulates the features of human COVID-19 disease progress and pathogenesis is greatly needed. In this study, we have comprehensively characterized a mouse model of SARS-CoV-2 infection using K18-hACE2 transgenic mice. We infected the mice with low and high doses of SARS-CoV-2 to study the pathogenesis and survival in response to different infection patterns. Moreover, we compared the pathogenesis of the K18-hACE2 transgenic mice with that of the COVID-19 patients to show that this model could be a useful tool for the development of antiviral drugs and therapeutics.
Topics: Angiotensin-Converting Enzyme 2; Animals; COVID-19; Disease Models, Animal; Humans; Immune Sera; Keratin-18; Mice; Mice, Transgenic; Promoter Regions, Genetic; Reinfection; SARS-CoV-2; Viral Proteins
PubMed: 34668775
DOI: 10.1128/JVI.00964-21 -
American Journal of Orthodontics and... Sep 2019
Topics: Antilymphocyte Serum; Data Collection; Kidney Transplantation; Sensitivity and Specificity
PubMed: 31474255
DOI: 10.1016/j.ajodo.2019.06.006 -
Methods in Molecular Biology (Clifton,... 2020The hemagglutination inhibition (HI) assay for influenza A virus has been used since the 1940s. The assay may be utilized to detect or quantify antibodies to influenza A...
The hemagglutination inhibition (HI) assay for influenza A virus has been used since the 1940s. The assay may be utilized to detect or quantify antibodies to influenza A viruses and can be used to characterize differences in antigenic reactivity between influenza isolates. In addition, data from HI assays are routinely used for antigenic cartography, influenza virus surveillance, epidemiology, and vaccine-seed strain selection. For antibody quantification, the HI assay is a fast and inexpensive method; other than a source of red blood cells, no expensive or unusual lab equipment is needed, and results can be obtained within a few hours. Historically, the HI assay has also served as a primary method of subtype identification and is still used widely. However, as gene sequencing technology has evolved to be cheaper and faster, it is replacing the HI assay for this purpose.
Topics: Animals; Antibodies, Viral; Antibody Specificity; Antigens, Viral; Chickens; Erythrocytes; Hemagglutination Inhibition Tests; Immune Sera
PubMed: 32170677
DOI: 10.1007/978-1-0716-0346-8_2 -
International Journal of Biological... Jun 2023Snakebite envenoming (SBE), a neglected tropical disease, claims lives of about 138,000 people globally, and antivenom is the only approved treatment worldwide. However,... (Review)
Review
Snakebite envenoming (SBE), a neglected tropical disease, claims lives of about 138,000 people globally, and antivenom is the only approved treatment worldwide. However, this century-old therapy has serious limitations, including limited efficacy and some side effects. Although alternative and adjunct therapies are being developed, their commercialization will take time. Hence, improving existing antivenom therapy is crucial for immediate reduction in the global SBE burden. The neutralization potential and immunogenicity of antivenoms depend primarily on the venom pool used for animal immunization and the production host, along with antivenom purification procedure and quality control. Enhancing antivenom quality and production capacity are also critical actions of the World Health Organization (WHO) roadmap 2021 against SBE. The present review details the latest developments in antivenom production, such as immunogen preparation, production host, antibody purification methods, antivenom testing-including alternative animal models, in vitro assays, and proteomics and in silico methodologies, and storage, reported from 2018 to 2022. Based on these reports, we propose that production of broadly specific, affordable, safe, and effective (BASE) antivenoms is fundamental to realizing the WHO roadmap and reducing the global SBE burden. This concept can also be applied during the designing of alternative antivenoms.
Topics: Animals; Antivenins; Snake Bites; Costs and Cost Analysis; Snakes; Snake Venoms
PubMed: 37072061
DOI: 10.1016/j.ijbiomac.2023.124478 -
Cell Reports Dec 2022Temperate phages dynamically switch between lysis and lysogeny in their full life cycle. Some Bacillus-infecting phages utilize a quorum-sensing-like intercellular...
Temperate phages dynamically switch between lysis and lysogeny in their full life cycle. Some Bacillus-infecting phages utilize a quorum-sensing-like intercellular communication system, the "arbitrium," to mediate lysis-lysogeny decisions. However, whether additional factors participate in the arbitrium signaling pathway remains largely elusive. Here, we find that the arbitrium signal induces the expression of a functionally conserved operon downstream of the arbitrium module in SPbeta-like phages. SPbeta yopM and yopR (as well as phi3T phi3T_93 and phi3T_97) in the operon play roles in suppressing phage lytic propagation and promoting lysogeny, respectively. We further focus on phi3T_93 and demonstrate that it directly binds antitoxin MazE in the host MazF/MazE toxin-antitoxin (TA) module and facilitates the activation of MazF's toxicity, which is required for phage suppression. These findings show events regulated by the arbitrium system and shed light on how the interplay between phages and the host TA module affects phage-host co-survival.
Topics: Antitoxins; Bacteriophages
PubMed: 36476854
DOI: 10.1016/j.celrep.2022.111752 -
Toxins Feb 2023Toxin-antitoxin (TA) systems are typically composed of a stable toxin and a labile antitoxin; the latter counteracts the toxicity of the former under suitable... (Review)
Review
Toxin-antitoxin (TA) systems are typically composed of a stable toxin and a labile antitoxin; the latter counteracts the toxicity of the former under suitable conditions. TA systems are classified into eight types based on the nature and molecular modes of action of the antitoxin component so far. The 10 pairs of TA systems discovered and experimentally characterised in are type II TA systems. Type II TA systems have various physiological functions, such as virulence and biofilm formation, protection host against antibiotics, persistence, plasmid maintenance, and prophage production. Here, we review the type II TA systems of , focusing on their biological functions and regulatory mechanisms, providing potential applications for the novel drug design.
Topics: Pseudomonas aeruginosa; Escherichia coli; Toxin-Antitoxin Systems; Toxins, Biological; Antitoxins; Bacterial Proteins
PubMed: 36828478
DOI: 10.3390/toxins15020164