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

Diversity of type II toxin-antitoxin systems in bacteria

Les systèmes toxine-antitoxine (TA) sont composés d’une toxine intracellulaire qui cible un processus cellulaire essentiel et qui est neutralisée par une antitoxine. Ces systèmes sont très abondant chez les bactéries et sont impliqués dans la réponse aux stress, la formation de biofilm, le phénomène de persistance, etc.Mon projet de thèse a porté sur l’étude de la diversité des systèmes TA à deux niveaux. Dans un premier temps, plusieurs toxines de la famille RelE provenant de différentes espèces bactériennes et associées à des antitoxines non-canoniques ont été étudiées. Dans la seconde partie de ma thèse, nous avons caractérisé l’activation spécifique de deux systèmes TA d’Escherichia coli au niveau de la régulation transcriptionnelle du système et de l’activation de la toxine.Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Diversity of type II toxin-antitoxin systems in bacteria

Les systèmes toxine-antitoxine (TA) sont composés d’une toxine intracellulaire qui cible un processus cellulaire essentiel et qui est neutralisée par une antitoxine. Ces systèmes sont très abondant chez les bactéries et sont impliqués dans la réponse aux stress, la formation de biofilm, le phénomène de persistance, etc.Mon projet de thèse a porté sur l’étude de la diversité des systèmes TA à deux niveaux. Dans un premier temps, plusieurs toxines de la famille RelE provenant de différentes espèces bactériennes et associées à des antitoxines non-canoniques ont été étudiées. Dans la seconde partie de ma thèse, nous avons caractérisé l’activation spécifique de deux systèmes TA d’Escherichia coli au niveau de la régulation transcriptionnelle du système et de l’activation de la toxine.Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Toxin-antitoxin systems as multilevel interaction systems.

Toxin-antitoxin (TA) systems are small genetic modules usually composed of a toxin and an antitoxin counteracting the activity of the toxic protein. These systems are widely spread in bacterial and archaeal genomes. TA systems have been assigned many functions, ranging from persistence to DNA stabilization or protection against mobile genetic elements. They are classified in five types, depending on the nature and mode of action of the antitoxin. In type I and III, antitoxins are RNAs that either inhibit the synthesis of the toxin or sequester it. In type II, IV and V, antitoxins are proteins that either sequester, counterbalance toxin activity or inhibit toxin synthesis. In addition to these interactions between the antitoxin and toxin components (RNA-RNA, protein-protein, RNA-protein), TA systems interact with a variety of cellular factors, e.g. toxins target essential cellular components, antitoxins are degraded by RNAses or ATP-dependent proteases. Hence, TA systems have the capacity to interact with each other at different levels. In this review, we will discuss the different interactions in which TA systems are involved and their implications in TA system functions and evolution.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: re.jinfo:eu-repo/semantics/publishe

Reassessing the Role of the Type II MqsRA Toxin-Antitoxin System in Stress Response and Biofilm Formation: mqsA Is Transcriptionally Uncoupled from mqsR.

Toxin-antitoxin (TA) systems are broadly distributed modules whose biological roles remain mostly unknown. The mqsRA system is a noncanonical TA system in which the toxin and antitoxins genes are organized in operon but with the particularity that the toxin gene precedes that of the antitoxin. This system was shown to regulate global processes such as resistance to bile salts, motility, and biofilm formation. In addition, the MqsA antitoxin was shown to be a master regulator that represses the transcription of the csgD, cspD, and rpoS global regulator genes, thereby displaying a pleiotropic regulatory role. Here, we identified two promoters located in the toxin sequence driving the constitutive expression of mqsA, allowing thereby excess production of the MqsA antitoxin compared to the MqsR toxin. Our results show that both antitoxin-specific and operon promoters are not regulated by stresses such as amino acid starvation, oxidative shock, or bile salts. Moreover, we show that the MqsA antitoxin is not a global regulator as suggested, since the expression of csgD, cspD and rpoS is similar in wild-type and ΔmqsRA mutant strains. Moreover, these two strains behave similarly in terms of biofilm formation and sensitivity to oxidative stress or bile salts.IMPORTANCE There is growing controversy regarding the role of chromosomal toxin-antitoxin systems in bacterial physiology. mqsRA is a peculiar toxin-antitoxin system, as the gene encoding the toxin precedes that of the antitoxin. This system was previously shown to play a role in stress response and biofilm formation. In this work, we identified two promoters specifically driving the constitutive expression of the antitoxin, thereby decoupling the expression of antitoxin from the toxin. We also showed that mqsRA contributes neither to the regulation of biofilm formation nor to the sensitivity to oxidative stress and bile salts. Finally, we were unable to confirm that the MqsA antitoxin is a global regulator. Altogether, our data are ruling out the involvement of the mqsRA system in Escherichia coli regulatory networks.info:eu-repo/semantics/publishe

Type II toxin-antitoxin loci :the ccdAB and parDE families

info:eu-repo/semantics/publishe

Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems.

Several reports mention the presence of antibiotic resistance genes in natural and polluted environments, but many studies are based on their detection via polymerase chain reaction (PCR amplification of known genes and not on an activity screening. We constructed a metagenomic fosmid bank from DNA isolated from a polluted river in Brussels, Belgium, the Zenne. A total of 120,000 clones were pooled and plated directly on solid media containing different antibiotics. Several clones were isolated which could grow in the presence of ampicillin. The DNA from several clones was extracted and subjected to restriction analysis and, based on their restriction pattern, two different clones were found. One of the clones was selected for further study as it showed a higher level of resistance to different β-lactams antibiotics (ticarcilline and ceftazidime). To find out which gene is responsible for the resistance, an in vitro transposon mutagenesis was performed and clones having lost the resistance phenotype were analyzed via inverse PCR amplification. Several clones had an insert in a gene encoding a new type of β-lactamase. The amplified fosmid DNA was fully sequenced revealing an insert of 41 kb containing 39 open reading frames (ORFs). Transposon insertions inactivating the resistance to β-lactams were also found in the ORF upstream of the blaA gene, encoding an aminotransferase, suggesting a polar effect on the transcription of the gene downstream. In addition, other genes were found such as histidine biosynthesis genes, which were found to be scattered on the insert, a relA/spoT gene, and genes belonging to type II toxin-antitoxin system. This predicted system was experimentally validated in Escherichia coli using an inducible expression system.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

A protocol for automated timber species identification using metabolome profiling

Using chemical fingerprints for timber species identification is a relatively new, but promising technique. However, little is known about the effect of pre-processing spectral data parameter settings on the timber species classification accuracy. Therefore, this study presents an extensive and automated analysis method using the random forest machine learning algorithm on a set of highly valuable timber species from the Meliaceae family. Metabolome profiles were collected using direct analysis in real-time (DART (TM)) ionisation coupled with time-of-flight mass spectrometry (TOFMS) analysis of heartwood specimens for 175 individuals (representing 10 species). In order to analyse variability in classification accuracy, 110 sets of data pre-processing parameter combinations consisting of mass tolerance for binning and relative abundance cut-off thresholds were tested. Furthermore, for each set of parameters (designated binning/threshold setting), a random search for one hyperparameter of interest was performed, i.e. the number of variables (in this case ions) drawn randomly for each random forest analysis. The best classification accuracy (82.2%) was achieved with 47 variables and a binning and threshold combination of 40mDa and 4%, respectively. Entandrophragma angolense is mostly confused with Entandrophragma candollei and Khaya anthotheca, and several Swietenia species are confused with each other due to the high similarity of their chemical fingerprints. Entandrophragma cylindricum, Entandrophragma utile, Khaya ivorensis, Lovoa trichilioides and Swietenia macrophylla are easy to discriminate and show less misclassifications. The choice of parameter settings, whether it is in the data pre-processing (binning and threshold) or classification algorithm (hyperparameters), results in variability in classification accuracy. Therefore, a preliminary parameter screening is proposed before constructing the final model when using the random forest algorithm for classification. Overall, DART-TOFMS in combination with random forest is a powerful tool for species identification

An Integrated Study on Analysis, Intelligence and Repair of Composite Structures with Damage(II)

本整合計劃將集合相關研究之教授，以分工合作方式研究受損複材結構(以樑、板為主)在受損(如脫層)後其結構之各種力學行為分析(層間應力、勁度、振頻與模態、挫曲負載與模態、強度)具偵測與控制前述力學行為功能之智慧結構的分析與設計、對受損複材結構加以修補之設計與分析，這些分工以各個子計劃分別進行；同時總計劃則進行協調合作討論、對各子計劃之工作和成果內容加以規範與整合，達成建立一套能用而有效之整合系統，可真正應用於針對複材結構受損後之各種力學行為分析，並對此行為之智慧監控、和修補之分析設計

Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen <i>Enterococcus faecalis</i>

<p>We discovered a chromosomal locus containing 2 toxin-antitoxin modules (TAs) with an antisense transcriptional organization in the E. faecalis clinical isolate V583. These TAs are homologous to the type I txpA-ratA system and the type II mazEF, respectively. We have shown that the putative MazF is toxic for E. coli and triggers RNA degradation, and its cognate antitoxin MazE counteracts toxicity. The second module, adjacent to mazEF, expresses a toxin predicted to belong to the TxpA type I family found in Firmicutes, and the antisense RNA antidote, RatA. Genomic analysis indicates that the cis-association of mazEF and txpA-ratA modules has been favored during evolution, suggesting a selective advantage for this TA organization in the E. faecalis species. We showed regulatory interplays between the 2 modules, involving transcription control and RNA stability. Remarkably, our data reveal that MazE and MazEF have a dual transcriptional activity: they act as autorepressors and activate ratA transcription, most likely in a direct manner. RatA controls txpA RNA levels through stability. Our data suggest a pivotal role of MazEF in the coordinated expression of mazEF and txpA-ratA modules in V583. To our knowledge, this is the first report describing a crosstalk between type I and II TAs.</p