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Toxin-antitoxins (TAs) are prokaryotic two-gene systems composed of a toxin neutralized by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilizes the antitoxin by recognizing its chaperone addiction (ChAD) element. TACs mediate antiphage defense, but the mechanisms of viral sensing and restriction are unexplored. We identify two Escherichia coli antiphage TAC systems containing host inhibition of growth (HigBA) and CmdTA TA modules, HigBAC and CmdTAC. HigBAC is triggered through recognition of the gpV major tail protein of phage λ. Chaperone HigC recognizes gpV and ChAD via analogous aromatic molecular patterns, with gpV outcompeting ChAD to trigger toxicity. For CmdTAC, the CmdT ADP-ribosyltransferase toxin modifies mRNA to halt protein synthesis and limit phage propagation. Finally, we establish the modularity of TACs by creating a hybrid broad-spectrum antiphage system combining the CmdTA TA warhead with a HigC chaperone phage sensor. Collectively, these findings reveal the potential of TAC systems in broad-spectrum antiphage defense. [Display omitted] • E. coli HigBAC and CmdTAC are translation-targeting phage immunity TAC systems • The HigC chaperone senses the phage λ major tail protein to trigger the HigB toxin • The CmdT ADP-ribosyltransferase toxin inhibits translation by modifying mRNA • HigC combined with CmdTA yields a hybrid broad-spectrum antiphage defense system Toxin-antitoxin-chaperone (TAC) systems have been shown to mediate antiphage defense via as-yet unexplored mechanisms. Focusing on two TACs encoded by Escherichia coli prophages—HigBAC and CmdTAC—Mets et al. dissect the mechanisms of phage recognition by the SecB-like chaperone phage sensor and phage restriction by the TA warhead. [ABSTRACT FROM AUTHOR]

[Display omitted] Toxin-antitoxin (TA) systems are widespread among bacteria, archaea and fungi. They are classified into six types (I-VI) and have recently been proposed as novel drug targets. This study aimed to screen the pathogen Acinetobacter baumannii , known for its alarming antimicrobial resistance, for TA systems and identified a CptBA-like type IV TA, one of the least characterized systems. In silico methods included secondary structure prediction, comparative genomics, multiple sequence alignment, and phylogenetic analysis, while in vitro strategies included plasmid engineering and expression of the TA system in Escherichia coli BL21, growth measurement, and transcription analysis with quantitative reverse-transcription polymerase chain reaction. Comparative genomics demonstrated the distribution of CptBA-like systems among Gram-negative bacteria, while phylogenetic analysis delineated two major groups, in each of which Acinetobacter spp. proteins clustered together. Sequence alignment indicated the conservation of cptA and cptB in 4,732 strains of A. baumannii in the same syntenic order. Using A. baumannii recombinant cptA and cptB , cloned under different promoters, confirmed their TA nature, as cptB expression was able to reverse growth inhibition by CptA in a dose-time dependent manner. Furthermore, transcriptional analysis of cptBA in clinical and standard A. baumannii strains demonstrated the downregulation of this system under oxidative and antibiotic stress. Combining in silico and in vitro studies confirmed the predicted TA nature of a cptBA -like system in A. baumannii. Transcriptional analysis suggests a possible role of cptBA in response to antibiotics and stress factors in A. baumannii , making it a promising drug target. [ABSTRACT FROM AUTHOR]

Arbitrium-coding phages use peptides to communicate and coordinate the decision between lysis and lysogeny. However, the mechanism by which these phages establish lysogeny remains unknown. Here, focusing on the SPbeta phage family's model phages phi3T and SPβ, we report that a six-gene operon called the "SPbeta phages repressor operon" (sro) expresses not one but two master repressors, SroE and SroF, the latter of which folds like a classical phage integrase. To promote lysogeny, these repressors bind to multiple sites in the phage genome. SroD serves as an auxiliary repressor that, with SroEF, forms the repression module necessary for lysogeny establishment and maintenance. Additionally, the proteins SroABC within the operon are proposed to constitute the transducer module, connecting the arbitrium communication system to the activity of the repression module. Overall, this research sheds light on the intricate and specialized repression system employed by arbitrium SPβ-like phages in making lysis-lysogeny decisions. [Display omitted] • SPbeta phages encode two master repressors, SroF and SroE, in the sro operon • Multiple SroF binding sites required for repression and maintenance of lysogeny • The sro operon consists of conserved repressor and variable transducer modules • The transducer module bridges the arbitrium signal to the repression module SPbeta Bacillus phages use arbitrium to coordinate lysis-lysogeny decisions via the sro operon. Brady et al. show that the operon encodes two master repressors that bind multiple sites of the phage genome to promote lysogeny. Three accessory proteins connecting the arbitrium signal to the repression module constitute the transducer module. [ABSTRACT FROM AUTHOR]

Abstract Shewanella benthica DB21MT-2 is an obligate piezophilic bacterium isolated from the sediment of the Mariana Trench at depth of 10,898 m. Here we report the complete genome sequence of S. benthica DB21MT-2, which consists of a single circular chromosome with the size of 4,353,505 bp and G + C content of 45.86%. Comparative genomic analysis reveals the strain possesses multiple pathways for energy generation as has been reported in other deep-sea bacteria. In addition, several genes predicted to be involved in flagellar synthesis or component of toxin-antitoxin system are specifically found in obligate piezophilic strains from hadal trench. The result is expected to provide novel information for a better understanding on bacterial obligate piezophilic life-style and on bacterial adaptation to hadal trench environment. [ABSTRACT FROM AUTHOR]

[Display omitted] Inga vera and Lysiloma tree legumes form nodules with Bradyrhizobium spp. from the japonicum group that represent novel genomospecies, for which we describe here using genome data, symbiovars lysilomae, lysilomaefficiens and ingae. Genes encoding Type three secretion system (TTSS) that could affect host specificity were found in ingae but not in lysilomae nor in lysilomaefficiens symbiovars and uptake hydrogenase hup genes (that affect nitrogen fixation) were observed in bradyrhizobia from the symbiovars ingae and lysilomaefficiens. nolA gene was found in the symbiovar lysilomaefficiens but not in strains from lysilomae. We discuss that multiple genes may dictate symbiosis specificity. Besides, toxin-antitoxin genes were found in the symbiosis islands in bradyrhizobia from symbiovars ingae and lysilomaefficiens. A limit (95%) to define symbiovars with nifH gene sequences was proposed here. [ABSTRACT FROM AUTHOR]

A toxin-antitoxin system,vp1842/vp1843, locates within a superintegron on theVibrio parahaemolyticusgenome chromosome I whose toxin genevp1843encodes a DNA nicking endonuclease. We found that thevp1843expression inEscherichia colicells strongly induced chromosomal DNA degradation. On the basis of these observations, we discuss a possible physiological role ofvp1842/vp1843inV. parahaemolyticus. [ABSTRACT FROM PUBLISHER]

Summary PhoH2 proteins are found in a diverse range of organisms that span the bacterial tree and little is known about this large protein family. PhoH2 proteins have two domains: An N-terminal PIN domain fused to a C-terminal PhoH domain. The genome of Mycobacterium tuberculosis encodes 48 PIN domains and 47 of these constitute the VapC components of the 47 VapBC toxin-antitoxins. The 48th member of the M . tuberculosis PIN domain array is found in the single PhoH2 protein encoded in the genome. All characterized PIN domain proteins are RNases and the PhoH domains are predicted ATPases. This fusion of a PIN domain with an ATPase reflects a much wider association between PIN domains and PhoH domains across many prokaryote genomes. Here, we examine PhoH2 proteins from M . tuberculosis , Mycobacterium smegmatis and a thermophilic homologue from Thermobispora bispora and we show that PhoH2 is a sequence-specific RNA helicase and RNAse. In addition, phoH2 from M . tuberculosis and M . smegmatis is part of a longer mRNA transcript which includes a small, unannotated open reading frame (ORF) upstream of the phoH2 gene. This small gene overlaps with the beginning of the phoH2 gene in a manner similar to the PIN domain toxin-antitoxin operons. We have annotated the upstream gene as phoAT and its putative promoter elements satisfy previously characterized consensus sequences at the −10 site. Conditional growth experiments carried out in M . smegmatis revealed a negative effect on growth by the expression of M . tuberculosis PhoH2 that was alleviated by co-expression of the PhoAT peptide. Thus in M . tuberculosis , PhoH2 represents a new variation on a type II PIN domain toxin-antitoxin systems such that the toxin-antitoxin is now coupled to an RNA helicase whose predicted biological function is to unwind and cleave RNA in a sequence specific manner. [ABSTRACT FROM AUTHOR]

Abstract: Toxin–antitoxin (TA) systems are widespread in bacteria and archaea and play important roles in a diverse range of cellular activities. TA systems have been broadly classified into 5 types and the targets of the toxins are diverse, but the most frequently used cellular target is mRNA. Toxins that target mRNA to inhibit translation can be classified as ribosome-dependent or ribosome-independent RNA interferases. These RNA interferases are sequence-specific endoribonucleases that cleave RNA at specific sequences. Despite limited sequence similarity, ribosome-independent RNA interferases belong to a limited number of structural classes. The MazF structural family includes MazF, Kid, ParE and CcdB toxins. MazF members cleave mRNA at 3-, 5- or 7-base recognition sequences in different bacteria and have been implicated in controlling cell death (programmed) and cell growth, and cellular responses to nutrient starvation, antibiotics, heat and oxidative stress. VapC endoribonucleases belong to the PIN-domain family and inhibit translation by either cleaving tRNAfMet in the anticodon stem loop, cleaving mRNA at -AUA(U/A)-hairpin-G- sequences or by sequence-specific RNA binding. VapC has been implicated in controlling bacterial growth in the intracellular environment and in microbial adaptation to nutrient limitation (nitrogen, carbon) and heat shock. ToxN shows structural homology to MazF and is also a sequence-specific endoribonuclease. ToxN confers phage resistance by causing cell death upon phage infection by cleaving cellular and phage RNAs, thereby interfering with bacterial and phage growth. Notwithstanding our recent progress in understanding ribonuclease action and function in TA systems, the environmental triggers that cause release of the toxin from its cognate antitoxin and the precise cellular function of these systems in many bacteria remain to be discovered. This article is part of a Special Issue entitled: RNA Decay mechanisms. [Copyright &y& Elsevier]

The article presents a study which designs and constructs six major toxin-antitoxin (TA) disruptants of Escherichia coli K-12 W3110. Among the cultivated disruptants, Δ high-frequency-persistence mutants BA (ΔhipBA) showed a longer life span than other disruptants. The said disruptant may also function as a bacteriostatic system based on the physiological analysis.