Phage host range and definition of genes implicated in Type III toxin-antitoxin-mediated abortive infection

Bacteria are under constant threat by their viral parasites, the bacteriophages (phages) and have evolved a range of anti-phage systems to defend themselves. One of these systems is termed abortive infection (Abi) where, upon phage infection, an Abi system may be activated which initiate a bacteriostatic or bactericidal response. While the infected bacteria do not obviously benefit from the activation of these systems, the cessation of bacterial growth or premature cellular suicide prevents the release of phage progeny. Thus Abi can be viewed as an altruistic process as only the remaining clonal bacterial population benefits. The Type III toxin-antitoxin systems have previously been shown to be involved in Abi, however the mechanisms through which these systems are activated are still poorly understood. A common approach to reveal the phage product involved in triggering these systems is to first determine the mutations that a previously sensitive phage evolves to escape after exposure to an Abi system. Analysis of viral "escape" mutants has been used in this study to try to elucidate the activation mechanism(s) of two Type III systems (ToxIN$_P$$_a$ and TenpIN$_P$$_l$) of several environmental phages. Several new phage products were identified in escape mutants as candidate factors involved in circumventing Abi – and possible roles in phage metabolism predicted. Furthermore, the genomes of several phages that could not evolve escapes, or were insensitive to Abi, are sequenced and these data exposed interesting curiosities regarding Abi (as well as the discovery of several novel and rare phages). Previously, no coliphage was identified that was capable of escape of the ToxIN$_P$$_a$ or TenpIN$_P$$_l$ systems. However, this study defined and characterised the first ToxIN$_P$$_a$ and TenpIN$_P$$_l$ coliphage escapes as well as a new method for isolating host-dependent coliphage escapes. Finally, multiple phages that infect the insect pathogen $\textit{Photorhabdus luminescens}$ TT01 (the bacterial strain from which the TenpIN$_P$$_l$ system originated) were isolated, genomically sequenced and characterised in terms of host range. The results revealed a large superfamily of flagellum-dependent phages that exhibit remarkable host promiscuity, possibly defining the most promiscuous phages thus far identified

Structure, Evolution, and Functions of Bacterial Type III Toxin-Antitoxin Systems.

Toxin-antitoxin (TA) systems are small genetic modules that encode a toxin (that targets an essential cellular process) and an antitoxin that neutralises or suppresses the deleterious effect of the toxin. Based on the molecular nature of the toxin and antitoxin components, TA systems are categorised into different types. Type III TA systems, the focus of this review, are composed of a toxic endoribonuclease neutralised by a non-coding RNA antitoxin in a pseudoknotted configuration. Bioinformatic analysis shows that the Type III systems can be classified into subtypes. These TA systems were originally discovered through a phage resistance phenotype arising due to a process akin to an altruistic suicide; the phenomenon of abortive infection. Some Type III TA systems are bifunctional and can stabilise plasmids during vegetative growth and sporulation. Features particular to Type III systems are explored here, emphasising some of the characteristics of the RNA antitoxin and how these may affect the co-evolutionary relationship between toxins and cognate antitoxins in their quaternary structures. Finally, an updated analysis of the distribution and diversity of these systems are presented and discussed.Work in the Salmond lab is supported by the BBSRC, UK; N.G. was supported by the Fonds National de la Recherche Luxembourg (9118191); B.C. was supported by a Cambridge International Scholarship from the Cambridge Commonwealth, European & International Trust; and A.D. was supported by a BBSRC -DTP studentship.This is the final version of the article. It first appeared from Molecular Diversity Preservation International via https://doi.org/10.3390/toxins810028

tert-Butyl 3-[N-(tert-butoxy­carbonyl)methyl­amino]-4-methoxy­imino-3-methyl­piperidine-1-carboxyl­ate

The title compound, C18H33N3O5, was prepared from N-tert-butoxy­carbonyl-4-piperidone using a nine-step reaction, including condensation, methyl­ation, oximation, hydrolysis, esterification, ammonolysis, Hoffmann degradation, tert-butoxy­carbonyl protection and methyl­ation. The E configuration of the methyl­oxime geometry of the compound is confirmed

Challenges of using protein antibiotics for pathogen control

Bacterial phytopathogens represent a significant threat to many economically important crops. Current control measures often inflict harm on the environment and may ultimately impact on human health through the spread of antibiotic resistance. Antimicrobial proteins such as bacteriocins have been suggested as the next generation of disease control agents since they are able to specifically target the pathogen of interest with minimal impact on the wider microbial community and environment. However, substantial gaps in knowledge with regards to the efficacy and application of bacteriocins to combat phytopathogenic bacteria remain. Here we highlight the immediate challenges the community must address to ensure maximum exploitation of antimicrobial proteins in the field

Bacteriocins targeting Gram-negative phytopathogenic bacteria: plantibiotics of the future

Gram-negative phytopathogenic bacteria are a significant threat to food crops. These microbial invaders are responsible for a plethora of plant diseases and can be responsible for devastating losses in crops such as tomatoes, peppers, potatoes, olives, and rice. Current disease management strategies to mitigate yield losses involve the application of chemicals which are often harmful to both human health and the environment. Bacteriocins are small proteinaceous antibiotics produced by bacteria to kill closely related bacteria and thereby establish dominance within a niche. They potentially represent a safer alternative to chemicals when used in the field. Bacteriocins typically show a high degree of selectivity toward their targets with no off-target effects. This review outlines the current state of research on bacteriocins active against Gram-negative phytopathogenic bacteria. Furthermore, we will examine the feasibility of weaponizing bacteriocins for use as a treatment for bacterial plant diseases

tert-Butyl 3-carbamoyl-4-methoxy­imino-3-methyl­piperidine-1-carboxyl­ate

In the title compound, C13H23N3O4, the piperidine ring adopts a chair conformation. An intra­molecular N—H⋯O hydrogen bond is observed between the carbamoyl and carboxyl­ate groups. In the crystal structure, mol­ecules form inversion dimers linked by pairs of N—H⋯O hydrogen bonds

Preclinical development of a bispecific TNFα/IL-23 neutralising domain antibody as a novel oral treatment for inflammatory bowel disease.

Anti-TNFα and anti-IL-23 antibodies are highly effective therapies for Crohn's disease or ulcerative colitis in a proportion of patients. V56B2 is a novel bispecific domain antibody in which a llama-derived IL-23p19-specific domain antibody, humanised and engineered for intestinal protease resistance, V900, was combined with a previously-described TNFα-specific domain antibody, V565. V56B2 contains a central protease-labile linker to create a single molecule for oral administration. Incubation of V56B2 with trypsin or human faecal supernatant resulted in a complete separation of the V565 and V900 monomers without loss of neutralising potency. Following oral administration of V900 and V565 in mice, high levels of each domain antibody were detected in the faeces, demonstrating stability in the intestinal milieu. In ex vivo cultures of colonic biopsies from IBD patients, treatment with V565 or V900 inhibited tissue phosphoprotein levels and with a combination of the two, inhibition was even greater. These results support further development of V56B2 as an oral therapy for IBD with improved safety and efficacy in a greater proportion of patients as well as greater convenience for patients compared with traditional monoclonal antibody therapies

Overuse of medications in low- and middle-income countries: a scoping review

OBJECTIVE: To identify and summarize the evidence about the extent of overuse of medications in low- and middle-income countries, its drivers, consequences and potential solutions. METHODS: We conducted a scoping review by searching the databases PubMed®, Embase®, APA PsycINFO® and Global Index Medicus using a combination of MeSH terms and free text words around overuse of medications and overtreatment. We included studies in any language published before 25 October 2021 that reported on the extent of overuse, its drivers, consequences and solutions. FINDINGS: We screened 3489 unique records and included 367 studies reporting on over 5.1 million prescriptions across 80 low- and middle-income countries – with studies from 58.6% (17/29) of all low-, 62.0% (31/50) of all lower-middle- and 60.0% (33/55) of all upper-middle-income countries. Of the included studies, 307 (83.7%) reported on the extent of overuse of medications, with estimates ranging from 7.3% to 98.2% (interquartile range: 30.2–64.5). Commonly overused classes included antimicrobials, psychotropic drugs, proton pump inhibitors and antihypertensive drugs. Drivers included limited knowledge of harms of overuse, polypharmacy, poor regulation and financial influences. Consequences were patient harm and cost. Only 11.4% (42/367) of studies evaluated solutions, which included regulatory reforms, educational, deprescribing and audit–feedback initiatives. CONCLUSION: Growing evidence suggests overuse of medications is widespread within low- and middle-income countries, across multiple drug classes, with few data of solutions from randomized trials. Opportunities exist to build collaborations to rigorously develop and evaluate potential solutions to reduce overuse of medications

A novel framework for making dominant point detection methods non-parametric

Most dominant point detection methods require heuristically chosen control parameters. One of the commonly used control parameter is maximum deviation. This paper uses a theoretical bound of the maximum deviation of pixels obtained by digitization of a line segment for constructing a general framework to make most dominant point detection methods non-parametric. The derived analytical bound of the maximum deviation can be used as a natural bench mark for the line fitting algorithms and thus dominant point detection methods can be made parameter-independent and non-heuristic. Most methods can easily incorporate the bound. This is demonstrated using three categorically different dominant point detection methods. Such non-parametric approach retains the characteristics of the digital curve while providing good fitting performance and compression ratio for all the three methods using a variety of digital, non-digital, and noisy curves