:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...

The Retron-Eco7 is a genetic element involved in anti-phage defense that encodes two effector proteins (PtuA and PtuB) and cleaves the host tRNA. Here, the authors solved the Retron-Eco7 complex struc...

Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...

Contractile injection systems (CISs) are derivatives of phage tails and widely distributed in prokaryotes. CISs load cognate effectors and eject them through contractile actions resembling those of phage tails. Ejected effectors play central roles in CIS functionality by acting on target cells and mediating various biological processes. Here, we report a novel group of CIS effectors related to phage tapemeasure protein, the transmembrane component of the phage infection machinery. This group is broadly distributed within the class actinobacteria, one of the bacterial classes in which CIS gene clusters are highly conserved, and is represented by Sle1, a cognate effector of the intracellularly localised Streptomyces lividans phage tail-like nanoparticle (SLP). This effector is associated with Sle2, which contains a CIS effector core domain and interacts with the SLP core component. Sle1 is packaged inside SLP and is translocated to lipid membranes along with SLPs. The functional domain of Sle1, probably through interactions with ribosome-containing subcellular fractions, upregulates the membrane-associated proteome in S. lividans and E. coli . This effect modifies the physiological properties of S. lividans , ultimately enhancing its adaptation to microbial competition. In addition, we revealed that Sle1-type effectors conserved among actinobacterial species are structurally and functionally diverse in their functional domains. One of them from Micromonospora eburnea constitutes a novel toxin-antitoxin system and introducing its functional domain into Sle1 reprogrammes the phenotypic responsiveness of S. lividans to neighbouring bacteria. Our findings illustrate that phage elements can be incorporated into CISs as reconfigurable platforms for bacterial adaptation to various environmental conditions.

Ye et al. define the structure and mechanisms of a bacterial pathway that performs ubiquitination-like protein conjugation, revealing new insights into the evolution and biological roles of ubiquitina...

We discover and study reverse transcriptases

The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific nuclease activity to restrict ...

Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

Bacteria rely on retrons for phage defense, yet most known systems come from clinical or lab strains. This study identifies new and diverse retrons from environmental bacteria, uncovering their phage defense mechanisms and applying them as genome editing tools.

Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...